Methods and compositions for long fragment read sequencing

ABSTRACT

The present invention is directed to methods and compositions for long fragment read sequencing. The present invention encompasses methods and compositions for preparing long fragments of genomic DNA, for processing genomic DNA for long fragment read sequencing methods, as well as software and algorithms for processing and analyzing sequence data.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of priority to U.S. PatentApplication No. 61/187,162, filed Jun. 15, 2009, and is acontinuation-in-part of U.S. patent application Ser. No. 12/329,365,filed Dec. 5, 2008, which claims the benefit of priority of 60/992,485,filed Dec. 5, 2007; 61/026,337, filed Feb. 5, 2008; 61/035,914, filedMar. 12, 2008; 61/061,134, filed Jun. 13, 2008; 61/116,193, filed Nov.19, 2008; 61/102,586, filed on Oct. 3, 2008; Ser. Nos. 12/265,593, filedNov. 5, 2008; and 12/266,385, filed Nov. 6, 2008, each of which ishereby incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

Large-scale genomic sequence analysis is a key step toward understandinga wide range of biological phenomena. The need for low-cost,high-throughput sequencing and re-sequencing has led to the developmentof new approaches to sequencing that employ parallel analysis ofmultiple nucleic acid targets simultaneously.

Conventional methods of sequencing are generally restricted todetermining a few tens of nucleotides before signals becomesignificantly degraded, thus placing a significant limit on overallsequencing efficiency. Conventional methods of sequencing are also oftenlimited by signal-to-noise ratios that render such methods unsuitablefor single-molecule sequencing.

It would be advantageous for the field if methods and compositions couldbe designed to increase the efficiency of sequencing reactions as wellas the efficiency of assembling complete sequences from shorter readlengths.

SUMMARY OF THE INVENTION

Accordingly, the present invention provides methods and compositions forsequencing reactions.

In an exemplary embodiment, the present invention provides a method offragmenting a double-stranded target nucleic acid. This method includes(a) providing genomic DNA; (b) dividing DNA into a number of separatealiquots; (c) amplifying the DNA in the separate aliquots in thepresence of a population of dNTPs that includes dNTP analogs, such thata number of nucleotides in the DNA are replaced by dNTP analogs; (d)removing the dNTP analogs to form gapped DNA; (e) treating the gappedDNA to translate the gaps until gaps on opposite strands converge,thereby creating blunt-ended DNA fragments. In a further embodiment,substantially every fragment in a separate mixture is non-overlappingwith every other fragment of the same aliquot.

In a further embodiment and in accordance with any of the above, thepresent invention provides a method for fragmenting nucleic acids thatincludes the steps of: (a) providing at least two genome-equivalents ofDNA for at least one genome; (b) dividing the DNA into a first tier ofseparate mixtures; (c) amplifying the DNA in the separate mixtures,wherein the amplifying is conducted with a population of dNTPs thatcomprises a predetermined ratio of dUTP to dTTP, such that a number ofthymines in said DNA are replaced by uracils, and a predetermined ratioof 5-methyl dCTP to dCTP, such that a number of cytosines are replacedby 5-methyl cytosines; (d) removing the uracils and the 5-methylcytosines to form gapped DNA; (e) treating the gapped DNA to translatesaid gaps until gaps on opposite strands converge, thereby creatingblunt-ended DNA fragments, where the blunt-ended fragments have less GCbias and less coverage bias as compared to fragments generated in theabsence of 5-methyl cytosine.

In a further embodiment, the present invention provides a method offragmenting a double-stranded target nucleic acid that includes thesteps of: (a) providing genomic DNA; (b) dividing the DNA into separatealiquots; (c) amplifying the DNA in the separate aliquots to form aplurality of amplicons, where the amplifying is conducted with apopulation of dNTPs that comprises dNTP analogs, such that a number ofnucleotides in the amplicons are replaced by the dNTP analogs; andwherein the amplifying is conducted in the presence of an additiveselected from glycogen, DMSO, ET SSB, betaine, and any combinationthereof; (c) removing the dNTP analogs from the amplicons to form gappedDNA; (d) treating the gapped DNA to translate said gaps until gaps onopposite strands converge, thereby creating blunt-ended DNA fragments,wherein the blunt-ended fragments have less GC bias as compared tofragments generated in the absence of the additive.

In a further embodiment, the present invention provides a method ofobtaining sequence information from a genome that includes the steps:(a) providing a population of first fragments of said genome; (b)preparing emulsion droplets of the first fragments, such that eachemulsion droplet comprises a subset of the population of firstfragments; (c) obtaining a population of second fragments within eachemulsion droplet, such that the second fragments are shorter than thefirst fragments from which they are derived; (d) combining the emulsiondroplets of the second fragments with emulsion droplets of adaptor tags;(e) ligating the second fragments with the adaptor tags to form taggedfragments; (f) combining the tagged fragments into a single mixture; (g)obtaining sequence reads from the tagged fragments, where the sequencereads include sequence information from the adaptor tags and thefragments to identify fragments from the same emulsion droplet, therebyproviding sequence information for the genome.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic illustration of an embodiment of a method forfragmenting nucleic acids.

FIG. 2 a schematic illustration of an embodiment of a method forfragmenting nucleic acids.

FIG. 3 is a graph of the effect of primer concentration on GC bias inMDA reactions.

FIG. 4 shows the effect of DMSO and primer concentration on variability(FIG. 4A) and GC bias (FIG. 4B) in MDA reactions.

FIG. 5 shows the effect of SSB (FIG. 5A) and betaine (FIG. 5B) on GCbias in MDA reactions.

FIG. 6 is a schematic illustration of an embodiment of the invention formaking circular nucleic acid templates comprising multiple adaptors.

FIG. 7 is a schematic illustration of an embodiment of the invention forcontrolling the orientation of adaptors inserted into target nucleicacids.

FIG. 8 is a schematic illustration of exemplary embodiments of differentorientations in which adaptors and target nucleic acid molecules can beligated to each other.

FIG. 9 is a schematic illustration of one aspect of a method forassembling nucleic acid templates of the invention.

FIG. 10 is a schematic illustration of components of adaptors that areuseful for controlling the way such adaptors are inserted into a targetnucleic acid.

FIG. 11 is a schematic illustration of an embodiment of an arm-by-armligation process for inserting adaptors into target nucleic acids. FIG.11A illustrates an exemplary embodiment of the arm-by-arm ligationprocess and FIG. 11B illustrates exemplary components of adaptor arms ofuse in this process.

FIG. 12 is a schematic illustration of possible orientations of adaptorinsertion.

FIG. 13 is a schematic illustration of one embodiment of a nicktranslation ligation method.

FIG. 14 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 15 is a schematic illustration of one embodiment of a nicktranslation ligation method.

FIG. 16 is a schematic illustration of one embodiment of a nicktranslation ligation method.

FIG. 17 is a schematic illustration of one embodiment of a nicktranslation ligation method utilizing nick translation circle inversion(FIG. 17A) and nick translation circle inversion combined with uracildegradation (FIG. 17B).

FIG. 18 is a schematic illustration of an embodiment of a nicktranslation ligation method.

FIG. 19 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 20 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 21 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 22 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 23 is a schematic illustration of one embodiment of a combinatorialprobe anchor ligation method.

FIG. 24 is a schematic illustration of one embodiment of a combinatorialprobe anchor ligation method.

FIG. 25 is a schematic illustration of one embodiment of a combinatorialprobe anchor ligation method.

FIG. 26 is a schematic illustration of one embodiment of a combinatorialprobe anchor ligation method.

FIG. 27 is a schematic illustration of one embodiment of a method fortagging nucleic acid fragments.

FIG. 28(A)-(F) is a schematic overview of steps of an embodiment of thelong fragment read method of the present invention.

FIG. 29 is a schematic overview of using an embodiment of long fragmentread technology of the present invention to define haplotypes.

FIG. 30A is a schematic overview of an embodiment of long fragment readtechnology of the present invention. FIG. 30B is a schematic overview ofan exemplary method of preparing fragments for long fragment readtechnology.

DETAILED DESCRIPTION OF THE INVENTION

The practice of the present invention may employ, unless otherwiseindicated, conventional techniques and descriptions of organicchemistry, polymer technology, molecular biology (including recombinanttechniques), cell biology, biochemistry, and immunology, which arewithin the skill of the art. Such conventional techniques includepolymer array synthesis, hybridization, ligation, and detection ofhybridization using a label. Specific illustrations of suitabletechniques can be had by reference to the example herein below. However,other equivalent conventional procedures can, of course, also be used.Such conventional techniques and descriptions can be found in standardlaboratory manuals such as Genome Analysis: A Laboratory Manual Series(Vols. I-IV), Using Antibodies: A Laboratory Manual, Cells: A LaboratoryManual, PCR Primer: A Laboratory Manual, and Molecular Cloning: ALaboratory Manual (all from Cold Spring Harbor Laboratory Press),Stryer, L, (1995) Biochemistry (4th Ed.) Freeman, New York, Gait,“Oligonucleotide Synthesis: A Practical Approach” 1984, IRL Press,London, Nelson and Cox (2000), Lehninger, Principles of Biochemistry3^(rd) Ed., W. H. Freeman Pub. New York, N.Y. and Berg et al. (2002)Biochemistry, 5^(th) Ed., W. H. Freeman Pub. New York, N.Y., all ofwhich are herein incorporated in their entirety by reference for allpurposes.

Note that as used herein and in the appended claims, the singular forms“a,” “an,” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “a polymerase”refers to one agent or mixtures of such agents, and reference to “themethod” includes reference to equivalent steps and methods known tothose skilled in the art, and so forth.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. All publications mentionedherein are incorporated herein by reference for the purpose ofdescribing and disclosing devices, compositions, formulations andmethodologies which are described in the publication and which might beused in connection with the presently described invention.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range is encompassed within the invention. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges is also encompassed within the invention, subject to anyspecifically excluded limit in the stated range. Where the stated rangeincludes one or both of the limits, ranges excluding either both ofthose included limits are also included in the invention.

In the following description, numerous specific details are set forth toprovide a more thorough understanding of the present invention. However,it will be apparent to one of skill in the art that the presentinvention may be practiced without one or more of these specificdetails. In other instances, well-known features and procedures wellknown to those skilled in the art have not been described in order toavoid obscuring the invention.

Although the present invention is described primarily with reference tospecific embodiments, it is also envisioned that other embodiments willbecome apparent to those skilled in the art upon reading the presentdisclosure, and it is intended that such embodiments be contained withinthe present inventive methods.

I. Overview

The present invention is directed to compositions and methods fornucleic acid identification and detection, which find use in a widevariety of applications as described herein. Such applications includesequencing of whole genomes, sequencing of multiple whole genomes, anddetecting specific target sequences, including single nucleotidepolymorphisms (SNPs) and gene targets of interest.

The present invention provides compositions and methods for isolatingand fragmenting nucleic acids from a sample. For some applications,fragments are produced using a Controlled Random Enzymatic (CoRE)approach. In general, the CoRE fragmentation method involves replacing anumber of nucleotides in target nucleic acids with modified nucleotidesor nucleotide analogs. The modified/analog nucleotides are then removedby enzymatic treatment to produce gapped nucleic acids. Furtherenzymatic treatment translates those gaps along the nucleic acid untilgaps on opposite strands converge, resulting in blunt-ended nucleic acidfragments. Fragments produced in accordance with the present inventioncan be reproducibly controlled for length, bias and coverage.

One method by which nucleotides are replaced in target nucleic acids inaccordance with the CoRE fragmentation approach is through amplificationof the original population of target nucleic acids. This amplificationis generally conducted in the presence of a population of dNTPs, wherethat population includes a predetermined ratio of dNTP analogs tonaturally-occurring nucleotides. For example, in CoRE methods in whichthymines are replaced by deoxyuracils, the target nucleic acids areamplified using a population of dNTPs that contains a predeterminedratio of dUTPs to dTTPs. The number of thymines that are replaced (andthus the length of the resultant fragments) can be controlled bymanipulating the ratio of dUTPs to dTTPs. Similarly, CoRE methods thatreplace cytosines with 5-methyl cytosines or that replace adenines withinosine would utilize populations of dNTPs doped with a predeterminedproportion of 5-methyl cytosines or inosines. As will be appreciated,CoRE methods can also utilize any combination of deoxyuracils, 5-methylcytosines, and inosines to replace multiple nucleotides within thenucleic acid.

Methods of amplification used for CoRE or to amplify any nucleic acidconstruct described herein can include a large number of amplificationmethods known in the art. In some applications, Multiple DisplacementAmplification (MDA) is used to amplify nucleic acids for use insequencing and other applications described in further detail herein.The present invention provides compositions and methods for MDA thatreduce the GC bias that is inherent to many amplification methods,particularly whole genome amplification methods. In some applications,methods of the present invention include MDA methods that utilizeadditives such as betaine, glycerol, and single strand binding proteinsto prevent or ameliorate GC bias.

Nucleic acids, including nucleic acid fragments produced in accordancewith the present invention, can be used in a number of sequencingapplications. In certain applications, sequence information is obtainedfrom nucleic acid fragments using Long Fragment Read (LFR) sequencing.Such methods include physical separation of long genomic DNA fragmentsacross many different aliquots such that the probability of any givenregion of the genome of both the maternal and paternal component in thesame aliquot is very rare. By placing a unique identifier in eachaliquot and analyzing many aliquot in the aggregate, long fragments ofDNA can be assembled into a diploid genome, e.g. the sequence of eachparental chromosome can be obtained. In certain LFR applications,emulsion droplets are used in which each droplet contains a small numberof fragments, and all the emulsion droplets together contain fragmentsrepresenting one or more copies or equivalents of an entire genome.Emulsion droplets containing nucleic acid fragments are combined withemulsion droplets containing adaptors. The combined droplets provide anenclosed space for ligation of adaptors to fragments, such thatdifferent combined droplets contain fragments tagged with differentadaptors. In some applications, two or more adaptor tag components arecontained in the adaptor droplets, such that upon combination with adroplet containing nucleic acid fragments, unique combinatorial tags areligated to the fragments. In applications utilizing droplets, reagentssuch as ligase and buffers can be included in the emulsion dropletscontaining the nucleic acid fragments, the droplets containing theadaptors, or in separate droplets that are then combined with thefragment and adaptor droplets. An advantage of using emulsion dropletsis that reduction of reaction volumes to picoliter levels provides areduction in the costs and time associated with producing LFR libraries.Aliquots of nucleic acids can also be distributed among differentcontainers or vessels, such as different wells in a multiwell microtiterplate for LFR sequencing.

Regardless of the method by which different LFR aliquot libraries areproduced and tagged, the resultant nucleic acids can then be sequencedusing methods known in the art and described in further detail herein.Sequence reads from individual fragments can be assembled using sequenceinformation from their associated tag adaptors to identify fragmentsfrom the same aliquot.

II. Preparation of Nucleic Acids

The present invention includes methods and compositions for isolatingnucleic acids from samples. By “nucleic acid” or “oligonucleotide” or“polynucleotide” or grammatical equivalents herein means at least twonucleotides covalently linked together. The nucleic acid may be DNA,both genomic and cDNA, RNA or a hybrid, where the nucleic acid containsany combination of deoxyribo- and ribo-nucleotides, and any combinationof bases, including uracil, adenine, thymine, cytosine, guanine,inosine, xathanine hypoxathanine, isocytosine, isoguanine, etc. As usedherein, the term “nucleotide” encompasses both nucleotides andnucleosides as well as nucleoside and nucleotide analogs, and modifiednucleotides such as amino modified nucleotides. In addition,“nucleotide” includes non-naturally occurring analog structures. Thus,for example, the individual units of a peptide nucleic acid, eachcontaining a base, may be referred to herein as a nucleotide.

In the present invention, as is further discussed herein, nucleotideanalogs are used in many embodiments. Nucleotide analogs include anynucleotide that can be incorporated into genomic DNA that allowssubsequent cleavage, either enzymatically or chemically. Thus dUTP isconsidered a nucleotide analog, because uracil is not normally in thedeoxy state. Inosine, and 5-methyl cytosine are also considered modifiednucleotides or nucleotide analogs. In addition, as further describedbelow, several bases of RNA can be incorporated into genomic DNA toallow subsequent cleavage by RNAse H, and thus in these embodiments,those RNA bases would be considered analogs for the purposes of thepresent invention. Nucleotide analogs may also include abasic residues,such as 2′-deoxyribosylformamide, 2′-doexyribose, 1′2′-dideoxyribofuranose or propanediol.

A nucleic acid of the present invention will generally containphosphodiester bonds, although in some cases, as outlined below (forexample in the construction of primers and probes such as label probes),nucleic acid analogs are included that may have alternate backbones,comprising, for example, phosphoramide (Beaucage et al., Tetrahedron49(10):1925 (1993) and references therein; Letsinger, J. Org. Chem.35:3800 (1970); Sprinzl et al., Eur. J. Biochem. 81:579 (1977);Letsinger et al., Nucl. Acids Res. 14:3487 (1986); Sawai et al, Chem.Lett. 805 (1984), Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988);and Pauwels et al., Chemica Scripta 26:141 91986)), phosphorothioate(Mag et al., Nucleic Acids Res. 19:1437 (1991); and U.S. Pat. No.5,644,048), phosphorodithioate (Briu et al., J. Am. Chem. Soc. 111:2321(1989), O-methylphosphoroamidite linkages (see Eckstein,Oligonucleotides and Analogues: A Practical Approach, Oxford UniversityPress), and peptide nucleic acid (also referred to herein as “PNA”)backbones and linkages (see Egholm, J. Am. Chem. Soc. 114:1895 (1992);Meier et al., Chem. Int. Ed. Engl. 31:1008 (1992); Nielsen, Nature,365:566 (1993); Carlsson et al., Nature 380:207 (1996), all of which areincorporated by reference). Other analog nucleic acids include thosewith bicyclic structures including locked nucleic acids (also referredto herein as “LNA”), Koshkin et al., J. Am. Chem. Soc. 120:13252 3(1998); positive backbones (Denpcy et al., Proc. Natl. Acad. Sci. USA92:6097 (1995); non-ionic backbones (U.S. Pat. Nos. 5,386,023,5,637,684, 5,602,240, 5,216,141 and 4,469,863; Kiedrowshi et al., Angew.Chem. Intl. Ed. English 30:423 (1991); Letsinger et al., J. Am. Chem.Soc. 110:4470 (1988); Letsinger et al., Nucleoside & Nucleotide 13:1597(1994); Chapters 2 and 3, ASC Symposium Series 580, “CarbohydrateModifications in Antisense Research”, Ed. Y. S. Sanghui and P. Dan Cook;Mesmaeker et al., Bioorganic & Medicinal Chem. Lett. 4:395 (1994); Jeffset al., J. Biomolecular NMR 34:17 (1994); Tetrahedron Lett. 37:743(1996)) and non-ribose backbones, including those described in U.S. Pat.Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series580, “Carbohydrate Modifications in Antisense Research”, Ed. Y. S.Sanghui and P. Dan Cook. Nucleic acids containing one or morecarbocyclic sugars are also included within the definition of nucleicacids (see Jenkins et al., Chem. Soc. Rev, (1995) pp 169 176). Severalnucleic acid analogs are described in Rawls, C & E News Jun. 2, 1997page 35. “Locked nucleic acids” (LNA™) are also included within thedefinition of nucleic acid analogs. LNAs are a class of nucleic acidanalogues in which the ribose ring is “locked” by a methylene bridgeconnecting the 2′-O atom with the 4′-C atom. All of these references arehereby expressly incorporated by reference in their entirety for allpurposes and in particular for all teachings related to nucleic acids.These modifications of the ribose-phosphate backbone may be done toincrease the stability and half-life of such molecules in physiologicalenvironments. For example, PNA:DNA and LNA-DNA hybrids can exhibithigher stability and thus may be used in some embodiments.

Target nucleic acids can be obtained from a sample using methods knownin the art. The term “target nucleic acid” refers to a nucleic acid ofinterest and unless otherwise specified is used interchangeably with theterms “nucleic acid” and “polynucleotide”. As will be appreciated, thesample may comprise any number of substances, including, but not limitedto, bodily fluids (including, but not limited to, blood, urine, serum,lymph, saliva, anal and vaginal secretions, perspiration and semen, ofvirtually any organism, with mammalian samples being preferred and humansamples being particularly preferred); environmental samples (including,but not limited to, air, agricultural, water and soil samples);biological warfare agent samples; research samples (i.e. in the case ofnucleic acids, the sample may be the products of an amplificationreaction, including both target and signal amplification as is generallydescribed in PCT/US99/01705, such as PCR amplification reaction);purified samples, such as purified genomic DNA, RNA, proteins, etc.; rawsamples (bacteria, virus, genomic DNA, etc.); as will be appreciated bythose in the art, virtually any experimental manipulation may have beendone on the sample. In one aspect, the nucleic acid constructs of theinvention are formed from genomic DNA. In certain embodiments, thegenomic DNA is obtained from whole blood or cell preparations from bloodor cell cultures.

In one aspect, target nucleic acids of the invention are genomic nucleicacids, although other target nucleic acids can be used, including mRNA(and corresponding cDNAs, etc.). Target nucleic acids include naturallyoccurring or genetically altered or synthetically prepared nucleic acids(such as genomic DNA from a mammalian disease model). Target nucleicacids can be obtained from virtually any source and can be preparedusing methods known in the art. For example, target nucleic acids can bedirectly isolated without amplification, isolated by amplification usingmethods known in the art, including without limitation polymerase chainreaction (PCR), multiple displacement amplification (MDA) (whichencompasses and is used interchangeably with the term stranddisplacement amplification (SDA)), rolling circle amplification (RCA)(which encompasses and is used interchangeably with the term rollingcircle replication (RCR)) and other amplification methodologies. Targetnucleic acids may also be obtained through cloning, including but notlimited to cloning into vehicles such as plasmids, yeast, and bacterialartificial chromosomes.

In some aspects, the target nucleic acids comprise mRNAs or cDNAs. Incertain embodiments, the target DNA is created using isolatedtranscripts from a biological sample. Isolated mRNA may be reversetranscribed into cDNAs using conventional techniques, again as describedin Genome Analysis: A Laboratory Manual Series (Vols. I-IV) or MolecularCloning: A Laboratory Manual.

Target nucleic acids may be single stranded or double stranded, asspecified, or contain portions of both double stranded or singlestranded sequence. Depending on the application, the nucleic acids maybe DNA (including genomic and cDNA), RNA (including mRNA and rRNA) or ahybrid, where the nucleic acid contains any combination of deoxyribo-and ribo-nucleotides, and any combination of bases, including uracil,adenine, thymine, cytosine, guanine, inosine, xathanine hypoxathanine,isocytosine, isoguanine, etc.

In some embodiments the target nucleic acids are genomic DNA, in manyembodiments mammalian genomic DNA and in particular human genomic DNA.In some cases, the genomic DNA may be obtained from normal somatictissue, germinal tissue, or in some cases from diseased tissue, such astumor tissue. In many embodiments, as outlined herein, a number ofgenome equivalents are used, generally from 1 to 30, with from 5 to 20being useful in many embodiments. Many embodiments utilize 10 genomeequivalents. Genome equivalents can comprise complete genomes from oneor more cells or can comprise an amount of DNA that covers the genome ofone or more cells (i.e., a single diploid cell has 2 genome equivalentsof DNA). In some embodiments, at least two genome equivalents are usedin methods of the invention in order to fully cover a diploid genome.

In an exemplary embodiment, genomic DNA is isolated from a targetorganism. By “target organism” is meant an organism of interest and aswill be appreciated, this term encompasses any organism from whichnucleic acids can be obtained, particularly from mammals, includinghumans, although in some embodiments, the target organism is a pathogen(for example for the detection of bacterial or viral infections).Methods of obtaining nucleic acids from target organisms are well knownin the art. Samples comprising genomic DNA of humans find use in manyaspects and embodiments of the present invention. In some aspects suchas whole genome sequencing, about 1 to about 100 or more genomeequivalents of DNA are preferably obtained to ensure that the populationof target DNA fragments sufficiently covers the entire genome. Thenumber of genome equivalents obtained may depend in part on the methodsused to further prepare fragments of the genomic DNA for use inaccordance with the present invention. For example, in the long fragmentread methods described further below, about 1 to about 50 genomeequivalents are generally utilized. In further embodiments, about 2-40,3-30, 4-20, and 5-10 genome equivalents are used in methods of theinvention. In still further embodiments, about 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 genome equivalents areused. For certain methods, about 1000 to about 100,000 genomeequivalents are generally utilized. For some methods in which noamplification is used prior to fragmenting, about 100,000 to about1,000,000 genome equivalents are used.

Libraries containing nucleic acid constructs or fragments generated froma population containing one or more genome equivalents will comprisetarget nucleic acids whose sequences, once identified and assembled,will provide most or all of the sequence of an entire genome.

Target nucleic acids are isolated using conventional techniques, forexample as disclosed in Sambrook and Russell, Molecular Cloning: ALaboratory Manual, cited supra.

In some embodiments, target nucleic acids are treated to protect themduring subsequent chemical or mechanical manipulations. For example, incertain embodiments, target nucleic acids are isolated in the presenceof (or combined after isolation) with spermidine or polyvinylpyrrolidone40 (PVP40) to protect them from shearing during mechanical manipulationssuch as pipetting. Such protection is of particular use for applicationsthat utilize long nucleic acid fragments, such as the LFR methodsdescribed in further detail below. In some cases, it is advantageous toprovide carrier DNA, e.g. unrelated circular synthetic double-strandedDNA, to be mixed and used with the sample DNA whenever only smallamounts of sample DNA are available and there is danger of lossesthrough nonspecific binding, e.g. to container walls and the like.

II.A. Fragmenting Target Nucleic Acids

In some aspects of the present invention, target nucleic acids arefragmented. Fragment sizes of the target nucleic acid can vary dependingon the source target nucleic acid and the library construction methodsused. For certain applications, longer fragments are of use in theinvention. Such longer fragments may range in size from about 100,000 toabout 1,000,000 nucleotides in length. In further embodiments, longerfragments are about 50,000; 100,000; 150,000; 200,000; 250,000; 300,000;350,000; 400,000; 450,000; 500,000; 700,000; 900,000; 1,000,000;1,500,000 nucleotides in length. In yet further embodiments, longerfragments range from about 150,000-950,000; 200,000-900,000;250,000-850,000; 300,000-800,000; 350,000-750,000; 400,000-700,000;450,000-650,000; and 500,000-600,000 nucleotides in length. For certainapplications, fragments in the range of from about 50 to about 600nucleotides in length are used in methods of the present invention. Infurther embodiments, these fragments are about 100, 200, 300, 400, 500,600, 700, 800, 900, 1000, 1200, 1400, 1600, 1800, and 2000 nucleotidesin length. In yet further embodiments, the fragments are 10-100, 50-100,50-300, 100-200, 200-300, 50-400, 100-400, 200-400, 300-400, 400-500,400-600, 500-600, 50-1000, 100-1000, 200-1000, 300-1000, 400-1000,500-1000, 600-1000, 700-1000, 700-900, 700-800, 800-1000, 900-1000,1500-2000, 1750-2000, and 50-2000 nucleotides in length.

Many mechanical and enzymatic fragmentation methods are well known inthe art. In many embodiments, shear forces created during lysis andextraction will mechanically generate fragments in the desired range.Further mechanical fragmentation methods include sonication andnebulization. Mechanical fragmentation methods have the advantage ofproducing fragments of a particular size range in a predictable manner.However, mechanical fragmentation approaches typically require large (>2μg) or volumes (>200 μL) of input nucleic acid. Thus, mechanicalfragmentation approaches are only used in single sample processing.

Enzymatic fragmentation methods can also be used to generate nucleicacid fragments, particularly shorter fragments of 1-5 kb in size.Enzymatic fragmentation methods include the use of endonucleases.Enzymatic methods can be used with modest quantities and volumes ofnucleic acids and are more amenable than mechanical fragmentationmethods to multi-sample processing. However, enzymatic fragmentationmethods are inherently prone to variability in the degree offragmentation, because to achieve consistent fragment size distributionsin such methods requires extremely careful control of enzyme activity,substrate amounts and concentrations, and digestion time.

In some embodiments, fragments of a particular size or in a particularrange of sizes are isolated. Such methods are well known in the art. Forexample, gel fractionation can be used to produce a population offragments of a particular size within a range of basepairs, for examplefor 500 base pairs±50 base pairs.

In some cases, particularly when it is desired to isolate long fragments(such as fragments from about 150 to about 750 kilobases in length), thepresent invention provides methods in which cells are lysed and theintact nucleic are pelleted with a gentle centrifugation step. Thenucleic acid, usually genomic DNA, is released through enzymaticdigestion, using for example proteinase K and RNase digestion overseveral hours. The resultant material is then dialyzed overnight ordiluted directly to lower the concentration of remaining cellular waste.Since such methods of isolating the nucleic acid does not involve manydisruptive processes (such as ethanol precipitation, centrifugation, andvortexing), the genomic nucleic acid remains largely intact, yielding amajority of fragments in excess of 100 kilobases.

II.A.1. CoRE Fragmentation

As discussed above, methods of fragmentation for use in the presentinvention include both mechanical and enzymatic fragmentation methods,as well as combinations of enzymatic and fragmentation methods. In oneaspect, the present invention provides a method of fragmentationreferred to herein as Controlled Random Enzymatic (CORE) fragmentation.The CoRE fragmentation methods described herein can be used alone or incombination with other mechanical and enzymatic fragmentation methodsknown in the art.

In general, the CoRE fragmentation method involves replacing a number ofnucleotides in target nucleic acids with nucleotide analogs. The nucleicacids containing the nucleotide analogs are then treated enzymaticallyor chemically to produce gapped nucleic acids. In certain embodiments,the enzymatic/chemical treatment excises the nucleotide analogs from thenucleic acids to form gapped nucleic acids. In certain embodiments, theenzymatic/chemical treatment produces a nick either immediately 3′ or 5′to the nucleotide analogs to form the gapped nucleic acids. “Gappednucleic acids” are generally double stranded nucleic acids containingnicks or gaps of a single nucleotide or multiple nucleotides in at leastone strand.

Further enzymatic treatment of the gapped nucleic acids translates thosegaps along the nucleic acid until gaps on opposite strands converge,resulting in blunt-ended nucleic acid fragments. Fragments produced inaccordance with the present invention can be reproducibly controlled forlength, bias and coverage. CoRE fragmentation has the advantages ofenzymatic fragmentation (such as the ability to use low amounts and/orvolumes of DNA) without many of its drawbacks (including sensitivity tovariation in substrate or enzyme concentration and sensitivity todigestion time).

In further embodiments, nucleotide analogs are introduced into nucleicacids by amplifying the nucleic acids in the presence of dNTPs thatinclude a predetermined ratio of nucleotide analogs to naturallyoccurring nucleotides. Amplification with this mixed population ofnucleotides and nucleotide analogs results in amplicons in which anumber of the naturally occurring nucleotides are replaced by anucleotide analog. The number of nucleotides replaced by the analogs arecontrolled by controlling the predetermined ratio of analog to naturallyoccurring nucleotides in the dNTPs used in the amplification process.This “predetermined ratio” is the proportion of analog to naturalnucleotide that is needed to produce fragments of the desired length.For example, if the starting nucleic acids are about 100,000 bases inlength, the predetermined ratio of analog to nucleotide ratio can beadjusted to replace the desired number of nucleotides to eventuallyproduce (in a non-limiting example) fragments of 10,000 bases in length(after treatment to produce gapped nucleic acids and then furthertreatment to produce double stranded fragments).

The number of nucleotides that are replaced in the amplicons bynucleotide analogs is controlled by manipulating the ratio of nucleotideanalogs to naturally occurring nucleotides in the population of dNTPsused in the amplification process. In some embodiments, the populationof dNTPs used in the amplification process to produce amplicons withnucleotides replaced by nucleotide analogs comprises about 0.05% toabout 30% nucleotide analogs. In further embodiments, the population ofdNTPs comprises about 0.1%-0.5%, 0.5%-0.7%, 1%-25%, 5%-20%, 10%-15%nucleotide analogs. In still further embodiments, the population ofdNTPs comprises at least about 0.5%, 0.75%, 1%, 2%, 3%, 4%, 5%, 6%, 7%,8%, 9%, 10%, 11%, 12%, 13%, 14%, 15% nucleotide analogs.

In some embodiments, about 0.01-5% of one or more species of nucleotides(A, C, G and/or T) are replaced by a nucleotide analog in accordancewith the methods described herein. In further embodiments, about0.05%-4%, 0.1%-3%, 0.2%-2%, 0.3%-1%, 0.4%-0.9%, 0.5%-0.8%, and 0.6%-0.7%of one or more species of nucleotides are replaced by a nucleotideanalog in accordance with the above-described methods. In still furtherembodiments, at least about 0.1%, 0.2%, 0.25%, 0.3%, 0.4%, 0.5%, 0.6%,0.7%, 0.75%, 0.8%, 0.9%, 1%, 2%, 3%, 4%, and 5% of one or more speciesof nucleotides are replaced by a nucleotide analog in accordance withthe above-described methods.

After the nucleic acids are amplified in the presence of dNTPscontaining a predetermined ratio of nucleotide analogs, the resultantamplicons have some naturally occurring nucleotides replaced bynucleotide analogs. The amplicons are then treated chemically or withone or more enzymes to either remove the nucleotide analogs or toproduce a nick in the amplicon either 5′ or 3′ to the nucleotide analogto produce gapped nucleic acids. The gapped nucleic acids are thentreated with an enzyme, generally a polymerase, to translate the gapsalong the length of the nucleic acids until gaps on opposite strandsconverge. This results in a population of blunt-ended double strandedfragments.

In some embodiments, the present invention provides CoRE methods inwhich thymines are replaced by uracils or deoxyuracils, the targetnucleic acids are amplified using a population of dNTPs that contains apredetermined ratio of dUTPs to dTTPs. As discussed above, the number ofthymines that are replaced (and thus the length of the resultantfragments) can be controlled by manipulating the ratio of dUTPs todTTPs—for example, a higher proportion of dUTPs in comparison to dTTPswill result in a greater number of thymines in the target nucleic acidsubstituted with uracil. The subsequent treatment to remove the dUTPs(or create nicks either 3′ or 5′ of the dUTPs) will then result inshorter fragments, because the substitutions will have occurred withgreater frequency along the nucleic acid. Similarly, CoRE methods thatreplace cytosines with 5-methyl cytosines or that replace adenines withinosine would utilize populations of dNTPs doped with a predeterminedproportion of 5-methyl cytosines or inosines. As will be appreciated,CoRE methods in accordance with the present invention can utilize anycombination of deoxyuracils, 5-methyl cytosines, and inosines to replacemultiple species of nucleotides along the nucleic acid with analogs.

In further embodiments, a dNTP population comprising 4% dUTP withrespect to dTTP is used to amplify nucleic acids to produce amplicons inwhich a proportion of the thymines are replaced with deoxyuracil. Such aconcentration of dUTP will generally result in an incorporation ofapproximately 0.05%-0.1% of the thymines in the resultant ampliconsbeing replaced with deoxyuracil. As discussed above, the amount ofdeoxyuracil incorporated into the amplicons can be tuned by theproportion of dUTP to dTTP included in the dNTPs used to amplify thenucleic acids. In certain embodiments, the population of dUTPs withrespect to dTTPs comprises about 0.1%-0.5%, 0.5%-0.8%, 1%-25%, 5%-20%,10%-15% dUTPs. In still further embodiments, the population of dNTPscomprises at least about 0.5%, 0.75% 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%,10%, 11%, 12%, 13%, 14%, 15% dUTPs.

In some embodiments, a combination of nucleotide analogs is used in theamplification step of the CoRE method, such that two different speciesof nucleotides are replaced by nucleotide analogs in the resultantamplicons. For example, in some embodiments, both thymines and cytosinesare replaced with nucleotide analogs. In further embodiments, thyminesare replaced by deoxyuracils and cytosines are replaced by 5-methylcytosines. As discussed above, a range of proportions of the analogs tothe naturally occurring nucleotides can be used to control the size ofthe fragments that result when the amplicons are treated to form gappednucleic acids and then the gapped nucleic acids are treated to formdouble stranded fragments. In certain embodiments, the same proportionof dUTP and 5-methyl cytosine is used with respect to the naturallyoccurring nucleotides. In other words, a dNTP population comprisingabout 0.05%-25% dUTP with respect to dTTP and 0.05%-25% 5-methylcytosine with respect to cytosine is used to create amplicons in which aproportion of the thymines and cytosines are replaced by thecorresponding analogs. In still further embodiments, the dNTP populationcomprises about 4-5% 5-methyl cytosine and 0.75-1% dUTP. In yet furtherembodiments, the population of dUTPs with respect to dTTPs and thepopulation of 5-methyl cytosine with respect to cytosine comprises about0.1%-0.5%, 0.5%-0.8%, 1%-25%, 5%-20%, 10%-15% dUTPs. In still furtherembodiments, the population of dUTPs with respect to dTTPs and thepopulation of 5-methyl cytosine with respect to cytosine comprises atleast about 0.5%, 0.75% 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%,12%, 13%, 14%, 15% dUTPs. As will be appreciated, the same proportion ordifferent proportions of dUTP to dTTP as compared to the proportions of5-methyl cytosine to cytosine can be used in this embodiment of theinvention. If different proportions are used when different nucleotideanalogs are used, then any combination of the above listed proportionscan be used to generate amplicons in which at least a portion of thenaturally occurring nucleotides are replaced by nucleotide analogs.

An exemplary CoRE fragmentation method is illustrated in FIG. 1. First,a nucleic acid 101 is subjected to an enzyme catalyzed multipledisplacement amplification (MDA) in the presence of dNTPs doped withdUTP or UTP in a defined ration to the dTTP. This results in thesubstitution of deoxyuracil (“dU”) or uracil (“U”) at defined andcontrollable proportions of the T positions in both strands of theamplification product (103). The U moieties are then excised (104),usually through use of one or more enzymes, including without limitationUDG, EndolV, EndoVllI, and T4PNK, to create single base gaps (alsoreferred to herein as “nicks”) with functional 5′ phosphate and 3′hydroxyl ends (105). The single base gaps will be created at an averagespacing defined by the frequency of U of dU in the MDA product.Treatment of the gapped nucleic acid (105) with a polymerase withexonuclease activity results in “translation” or “translocation” of thenicks or gaps along the length of the nucleic acid until nicks onopposite strands converge, thereby creating double strand breaks,resulting a relatively population of double stranded fragments of arelatively homogenous size (107). The exonuclease activity of thepolymerase (such as Taq polymerase) will excise the short DNA strandthat abuts the nick while the polymerase activity will “fill in” thenick and subsequent nucleotides in that strand (essentially, the Taqmoves along the strand, excising bases using the exonuclease activityand adding the same bases, with the result being that the nick or gap istranslocated along the strand until the enzyme reaches the end). Thesize distribution of the double stranded fragments (107) is a result ofthe ratio of dTTP to dUTP or UTP used in the MDA reaction, rather thanby the duration or degree of enzymatic treatment. That is, the higherthe amount of dUTP, the shorter the resulting fragments. Thus, CoREfragmentation methods produce high degrees of fragmentationreproducibility as compared to other enzymatic or mechanicalfragmentation methods.

As will be appreciated, in the above exemplary embodiment and in anyembodiment of the CoRE method, a number of amplification methods can beused in the step to replace nucleotides with modified nucleotides ornucleotide analogs. Such amplification methods are described in furtherdetail below and can include without limitation polymerase chainreaction (PCR), multiple displacement amplification (MDA), rollingcircle amplification (RCA) (for circularized fragments), as well as anyother applicable amplification methods known in the art. As will also bediscussed in further detail below, in certain embodiments the methodsand compositions of the amplification reactions used in this step of theCoRE method can also reduce bias and increase coverage of the resultantfragments.

A further exemplary embodiment of a CoRE fragmentation method isillustrated in FIG. 2. In this exemplary embodiment, two differentnucleotides are replaced by nucleotide analogs: thymines are replaced byuracil and cytosines are replaced by 5-methyl cytosine. As illustratedin FIG. 2, a nucleic acid 201 is subjected to an enzyme catalyzedmultiple displacement amplification (MDA) in the presence of dNTPs dopedwith dUTP or UTP in a defined ratio to dTTP. The dNTPs are also dopedwith 5-methyl-dCTP at a defined proportion of the dCTP. This results inthe substitution of dU and 5-methyl dC at a defined (and controllable)proportion of T and C positions in both strands of the DNA product(203). Next, the U and regions near 5-methyl C moieties are excised—inone non-limiting example, the excision (204) is accomplished by acombination of McrBC, UDG and EndoIV or EndoVIII and T4PNK, to createsingle base gaps with functional 5′PO₄ and 3′OH ends (or in the case ofMcrBC double strand cuts), at a mean spacing defined by the frequency ofuracil and 5-methyl cytosine in the MDA product (203). The single basegaps will be created at an average spacing defined by the frequency of Uof dU in the MDA product. Treatment of the gapped nucleic acid (205)with a polymerase such as Taq polymerase or E. coli DNA pol I (206)results in translation of the gaps until gaps on opposite strandsconverge, thereby creating double strand breaks (207). Treatment with E.coli DNA pol I also fills in or removes any overhangs created fromdouble strand excision by McrBC. As in the method illustrated in FIG. 1,this exemplary embodiment of CoRE results in double stranded fragmentswhose length can be reproducibly controlled by altering the proportionof nucleotide analogs included in the population of dNTPs duringamplification. The introduction of the additional nucleotide analog(5-methyl cytosine) in this embodiment of CoRE improves fragmenting inGC-rich regions of the genome as compared to methods in which only asingle species of nucleotide analog is introduced into the targetnucleic acid. For example, the embodiment of CoRE illustrated in FIG. 1can show a bias towards higher fragmenting in AT rich regions of thegenome. Embodiments of CoRE in which more than one nucleotide analog isintroduced, such as the embodiment illustrated in FIG. 2, reducecoverage biases that can be observed in embodiments in which only asingle species of nucleotide analog is used or in other enzymatic and/ormechanical fragmentation methods.

As will be appreciated, any nucleotide analogs and modified nucleotidesknown in the art can be used to produce nucleic acid fragments inaccordance with the CoRE methods described above. In addition to theuracil and 5-methyl cytosine nucleotide analogs discussed above, furtherexemplary modified nucleotides and nucleotide analogs that can be of usein the CoRE methods of the present invention include without limitationpeptide nucleotides, modified peptide nucleotides, modifiedphosphate-sugar backbone nucleotides, N-7-methylguanine, deoxyuridineand deoxy-3′-methyladenosine.

II.B. Further Enzymatic and Chemical Treatment of Fragments

In some embodiments, after fragmenting, target nucleic acids are furthermodified to prepare them for later applications, such as in thepreparation of nucleic acid constructs as discussed in further detailbelow. Such modifications can be necessary because the process offragmentation may result in target nucleic acids with termini that arenot amenable to certain reactions, particularly the use of enzymes suchas ligases and polymerases. As for all the steps outlined herein, thisstep of further modification is optional and can be combined with anyother step in any order.

In an exemplary embodiment, after fragmenting, target nucleic acidsfrequently have a combination of blunt and overhang ends as well ascombinations of phosphate and hydroxyl chemistries at the termini. Suchfragments can be treated with several enzymes to create blunt ends withparticular chemistries. In one embodiment, a polymerase and dNTPs isused to fill in any 5′ single strands of an overhang to create a bluntend. Polymerase with 3′ exonuclease activity (generally but not alwaysthe same enzyme as the 5′ active one, such as T4 polymerase) is used toremove 3′ overhangs. Suitable polymerases include, but are not limitedto, T4 polymerase, Taq polymerases, E. coli DNA Polymerase 1, Klenowfragment, reverse transcriptases, φ29 related polymerases including wildtype φ29 polymerase and derivatives of such polymerases, T7 DNAPolymerase, T5 DNA Polymerase, RNA polymerases. These techniques can beused to generate blunt ends, which are useful in a variety ofapplications.

In further optional embodiments, the chemistry at the termini is alteredto avoid target nucleic acids from ligating to each other. For example,in addition to a polymerase, a protein kinase can also be used in theprocess of creating blunt ends by utilizing its 3′ phosphatase activityto convert 3′ phosphate groups to hydroxyl groups. Such kinases caninclude without limitation commercially available kinases such as T4kinase, as well as kinases that are not commercially available but havethe desired activity.

Similarly, a phosphatase can be used to convert terminal phosphategroups to hydroxyl groups. Suitable phosphatases include, but are notlimited to, Alkaline Phosphatase (including Calf Intestinal (CIP)),Antarctic Phosphatase, Apyrase, Pyrophosphatase, Inorganic (yeast)thermostable inorganic pyrophosphatase, and the like, which are known inthe art and commercially available, for example from New EnglandBiolabs.

As will be appreciated by those in the art, and as for all the stepsoutlined herein, any combination of these steps and enzymes may be used.For example, some enzymatic fragmentation techniques, such as the use ofrestriction endonucleases, may render one or more of these enzymatic“end repair” steps superfluous.

The modifications described above can prevent the creation of nucleicacid templates containing different fragments ligated in an unknownconformation, thus reducing and/or removing the errors in sequenceidentification and assembly that can result from templates generatedfrom such undesirable configurations.

In further embodiments, DNA fragments are denatured after fragmentationto produce single stranded fragments.

II.C. Amplification

In one embodiment, after fragmenting, (and in fact before or after anystep outlined herein) an amplification step can be applied to thepopulation of fragmented nucleic acids to ensure that a large enoughconcentration of all the fragments is available for subsequentapplications. Such amplification methods are well known in the art andinclude without limitation: polymerase chain reaction (PCR), ligationchain reaction (sometimes referred to as oligonucleotide ligaseamplification OLA), cycling probe technology (CPT), multipledisplacement amplification (MDA), transcription mediated amplification(TMA), nucleic acid sequence based amplification (NASBA), rolling circleamplification (RCA) (for circularized fragments), and invasive cleavagetechnology. As used herein, MDA encompasses and is used interchangeablywith the term “strand displacement amplification (SDA)”.

II.C.1. Multiple Displacement Amplification (MDA)

In one aspect of the invention, MDA is used to amplify fragments ornucleic acid constructs generated according to methods described herein.MDA generally involves bringing into contact at least one primer, DNApolymerase, and a target sample, and incubating the target sample underconditions that promote replication of the target sequence. If oneprimer is used (e.g. a “Watson” primer, complementary to the “Crick”target), multiple copies of one strand (e.g. “Crick”) of the doublestranded target are generated; if a second primer (e.g. “Crick”), whichis complementary to the second strand (e.g. “Watson”) of the target,then amplification of both strands occurs. Replication of the targetsequence results in replicated strands such that, during replication,the replicated strands are displaced from the target sequence by stranddisplacement replication of another replicated strand. In someembodiments of MDA, a random set of primers is used to randomly prime asample of genomic nucleic acid (or another sample of nucleic acid ofhigh complexity). By choosing a sufficiently large set of primers ofrandom or partially random sequence, the primers in the set will becollectively, and randomly, complementary to nucleic acid sequencesdistributed throughout nucleic acids in the sample. Amplificationproceeds by replication with a highly processive polymerase initiatingat each primer and continuing until spontaneous termination. A keyfeature of this method is the displacement of intervening primers duringreplication by the polymerase. In this way, multiple overlapping copiesof the entire genome can be synthesized in a short time. General methodsfor MDA are known in the art and disclosed for example in U.S. Pat. No.7,074,600, which is hereby incorporated by reference in its entirety forall purposes and in particular for all teachings related to MDA.

One weakness of conventional MDA methods, particularly when used forwhole genome amplification, is that a bias is often introduced into theamplification products. In many cases, this bias is a GC bias in which agreater number of copies are generated of regions of the genomicsequence that are GC-rich. In some cases, an AT bias is seen in whichAT-rich regions of the genome are amplified in greater quantities thanother sequences. The present invention provides compositions and methodsthat ameliorate or prevent bias that can result in amplificationreactions, particularly MDA reactions.

In some embodiments, rather than the random hexamers conventionally usedin MDA reactions, random 8-mer primers are used to reduce amplificationbias in the population of fragments. In addition, the primers used inMDA reactions can be designed to have a lower GC content, which also hasthe effect of lowering the GC bias. For example, FIG. 3 shows the effectof primer concentration on GC bias. In FIG. 3, points above the x-axisrepresent bias towards AT rich sequences and points below the x-axisshow bias toward GC rich sequences. Low GC content 6-mers (squares inFIG. 3) show relatively low bias across a wide range of concentrationsin MDA reactions conducted at 30° C. for 90 minutes.

In further embodiments, certain enzymes can be added to the MDA reactionto reduce the bias of the amplification. For example, low concentrationsof non-processive 5′ exonucleases can reduce GC-bias.

In still further embodiments, additives are included in the MDAreactions to prevent or ameliorate GC bias. Such additives includewithout limitation single-stranded binding proteins, betaine, DMSO,trehalose, glycerol.

FIG. 4 demonstrates that DMSO reduces the GC bias caused in MDAreactions by higher concentrations of primers (see FIG. 4B). As will beappreciate, a wide range of concentrations of DMSO can be used inaccordance with the invention. In exemplary non-limiting embodiments,about 0.5% to about 10% DMSO are used as an additive in MDA reactions ofthe invention. In still further embodiments, about 1%, 2%, 3%, 4%, 5%,6%, 7%, 8%, 10% DMSO is used in methods of the invention. In yet furtherembodiments, about 1%-2%, 2%-4%, 5%-8%, and 3%-6% DMSO is used.

FIG. 5 shows that both SSB (FIG. 5A) and betaine (FIG. 5B) can reduce GCbias across a wide range of concentrations. The experiments for FIGS. 4and 5 were conducted at 30° C. for 90 minutes. As will be appreciated, awide range of concentrations of SSB and betaine can be used inaccordance with the invention. In some embodiments, about 1 to about5000 ng of SSB are used in accordance with the invention. In furtherembodiments, about 1-10, 20-4000, 30-3000, 40-2000, 50-1000, 60-500,70-400, 80-300, 90-200, 10-100, 15-90, 20-80, 30-70, 40-60 ng of SSB areused. In some embodiments, about 0.1 to about 5 μM betaine is used inaccordance with the present invention. In further embodiments, about0.2-4, 0.5-3, and 1-2 μM betaine is used. In still further embodiments,about 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4and 1.5 μM betaine is used.

In certain embodiments, nucleic acid fragments are combined withspermidine prior to amplification with MDA in order to protect fromshearing during pipetting or other physical manipulations. However, highconcentrations of spermidine can interfere with MDA. In certainembodiments, prior to MDA, nucleic acid fragments are denatured in thepresence of a high concentration (˜100 mM) spermidine. The mixture isthen diluted to result in a 1 mM final concentration of spermidine andthen amplified using MDA or other amplification methods known in theart.

As will be appreciated, methods for preventing or ameliorating bias inMDA reactions can be used with any of the methods for fragmentingnucleic acids or generating nucleic acid constructs for production ofDNA nanoballs where those methods include one or more amplificationsteps.

II.D. Preparation of Circular Constructs

In one aspect, nucleic acid fragments produced as described above can beused to produce circular nucleic acid template constructs. Thesecircular constructs can serve as templates for the generation of DNAnanoballs, which are described in further detail below. The presentinvention provides circular nucleic acid template constructs comprisingtarget nucleic acids and multiple interspersed adaptors. The nucleicacid template constructs are assembled by inserting adaptors moleculesat a multiplicity of sites throughout each target nucleic acid fragment.The interspersed adaptors permit acquisition of sequence informationfrom multiple sites in the target nucleic acid consecutively orsimultaneously.

Although the embodiments of the invention described herein are generallydescribed in terms of circular nucleic acid template constructs, it willbe appreciated that nucleic acid template constructs may also be linear.Furthermore, nucleic acid template constructs of the invention may besingle- or double-stranded, with the latter being preferred in someembodiments. As used herein, unless otherwise noted, the term “targetnucleic acid” and “target nucleic acid fragments” and all grammaticalequivalents are used interchangeably.

The nucleic acid templates (also referred to herein as “nucleic acidconstructs” and “library constructs”) of the invention comprise targetnucleic acids and adaptors. As used herein, the term “adaptor” refers toan oligonucleotide of known sequence. Adaptors of use in the presentinvention may include a number of elements. The types and numbers ofelements (also referred to herein as “features”) included in an adaptorwill depend on the intended use of the adaptor. Adaptors of use in thepresent invention will generally include without limitation sites forrestriction endonuclease recognition and/or cutting, particularly TypeIIs recognition sites that allow for endonuclease binding at arecognition site within the adaptor and cutting outside the adaptor asdescribed below, sites for primer binding (for amplifying the nucleicacid constructs) or anchor primer (sometimes also referred to herein as“anchor probes”) binding (for sequencing the target nucleic acids in thenucleic acid constructs), nickase sites, and the like. In someembodiments, adaptors will comprise a single recognition site for arestriction endonuclease, whereas in other embodiments, adaptors willcomprise two or more recognition sites for one or more restrictionendonucleases. As outlined herein, the recognition sites are frequently(but not exclusively) found at the termini of the adaptors, to allowcleavage of the double stranded constructs at the farthest possibleposition from the end of the adaptor.

In some embodiments, adaptors will not include any recognition sites forrestriction endonucleases.

In some embodiments, adaptors of the invention have a length of about 10to about 250 nucleotides, depending on the number and size of thefeatures included in the adaptors. In certain embodiments, adaptors ofthe invention have a length of about 50 nucleotides. In furtherembodiments, adaptors of use in the present invention have a length ofabout 20 to about 225, about 30 to about 200, about 40 to about 175,about 50 to about 150, about 60 to about 125, about 70 to about 100, andabout 80 to about 90 nucleotides.

In further embodiments, adaptors may optionally include elements suchthat they can be ligated to a target nucleic acid as two “arms”. One orboth of these arms may comprise an intact recognition site for arestriction endonuclease, or both arms may comprise part of arecognition site for a restriction endonuclease.

In the latter case, circularization of a construct comprising a targetnucleic acid bounded at each termini by an adaptor arm will reconstitutethe entire recognition site.

In still further embodiments, adaptors of use in the invention willcomprise different anchor binding sites at their 5′ and the 3′ ends ofthe adaptor. As described further herein, such anchor binding sites canbe used in sequencing applications, including the combinatorial probeanchor ligation (cPAL) method of sequencing, described herein and inU.S. Application Nos. 60/992,485; 61/026,337; 61/035,914; 61/061,134;61/116,193; 61/102,586; Ser. Nos. 12/265,593; and 12/266,385 11/938,106;11/938,096; 11/982,467; 11/981,804; 11/981,797; 11/981,793; 11/981,767;11/981,761; 11/981,730; 11/981,685; 11/981,661; 11/981,607; 11/981,605;11/927,388; 11/927,356; 11/679,124; 11/541,225; 10/547,214; and11/451,691, all of which are hereby incorporated by reference in theirentirety, and particularly for disclosure relating to sequencing byligation.

In one aspect, adaptors of the invention are interspersed adaptors. By“interspersed adaptors” is meant herein oligonucleotides that areinserted at spaced locations within the interior region of a targetnucleic acid. In one aspect, “interior” in reference to a target nucleicacid means a site internal to a target nucleic acid prior to processing,such as circularization and cleavage, that may introduce sequenceinversions, or like transformations, which disrupt the ordering ofnucleotides within a target nucleic acid.

II.D.1. Overview of Template Construction Process

The nucleic acid template constructs of the invention contain multipleinterspersed adaptors inserted into a target nucleic acid, and in aparticular orientation. As discussed further herein, the target nucleicacids are produced from nucleic acids isolated from one or more cells,including one to several million cells. These nucleic acids are thenfragmented using mechanical or enzymatic methods. In specificembodiments, nucleic acid fragments produced using CoRE methodsdescribed herein are used to produce nucleic acid template constructs ofthe invention.

The target nucleic acid that becomes part of a nucleic acid templateconstruct of the invention may have interspersed adaptors inserted atintervals within a contiguous region of the target nucleic acids atpredetermined positions. The intervals may or may not be equal. In someaspects, the accuracy of the spacing between interspersed adaptors maybe known only to an accuracy of one to a few nucleotides. In otheraspects, the spacing of the adaptors is known, and the orientation ofeach adaptor relative to other adaptors in the library constructs isknown. That is, in many embodiments, the adaptors are inserted at knowndistances, such that the target sequence on one termini is contiguous inthe naturally occurring genomic sequence with the target sequence on theother termini. For example, in the case of a Type IIs restrictionendonuclease that cuts 16 bases from the recognition site, located 3bases into the adaptor, the endonuclease cuts 13 bases from the end ofthe adaptor. Upon the insertion of a second adaptor, the target sequence“upstream” of the adaptor and the target sequence “downstream” of theadaptor are actually contiguous sequences in the original targetsequence.

The present invention provides nucleic acid templates comprising atarget nucleic acid containing one or more interspersed adaptors. In afurther embodiment, nucleic acid templates formed from a plurality ofgenomic fragments can be used to create a library of nucleic acidtemplates. Such libraries of nucleic acid templates will in someembodiments encompass target nucleic acids that together encompass allor part of an entire genome. That is, by using a sufficient number ofstarting genomes (e.g. cells), combined with random fragmentation, theresulting target nucleic acids of a particular size that are used tocreate the circular templates of the invention sufficiently “cover” thegenome, although as will be appreciated, on occasion, bias may beintroduced inadvertently to prevent the entire genome from beingrepresented.

The nucleic acid template constructs of the invention comprise multipleinterspersed adaptors, and in some aspects, these interspersed adaptorscomprise one or more recognition sites for restriction endonucleases. Ina further aspect, the adaptors comprise recognition sites for nickingendonucleases, Type I endonucleases, Type II endonucleases, and/or TypeIII endonucleases such as EcoP1 and EcoP15). In further aspect, theadaptors comprise recognition sites for Type IIs endonucleases. Type-IIsand Type III endonucleases are generally commercially available and arewell known in the art. Such endonucleases recognize specific sequencesof nucleotide base pairs within a double stranded polynucleotidesequence. Upon recognizing that sequence, the Type IIs endonucleaseswill cleave the polynucleotide sequence, generally leaving an overhangof one strand of the sequence, or “sticky end.” Type-IIs and Type IIIendonucleases generally cleave outside of their recognition sites; thedistance may be anywhere from about 2 to 30 nucleotides away from therecognition site depending on the particular endonuclease. Some Type-IIsendonucleases are “exact cutters” that cut a known number of bases awayfrom their recognition sites. In some embodiments, Type IIsendonucleases are used that are not “exact cutters” but rather cutwithin a particular range (e.g. 6 to 8 nucleotides). Generally, Type IIsrestriction endonucleases of use in the present invention have cleavagesites that are separated from their recognition sites by at least sixnucleotides (i.e. the number of nucleotides between the end of therecognition site and the closest cleavage point). Exemplary Type IIsrestriction endonucleases include, but are not limited to, Eco57M I, MmeI, Acu I, Bpm I, BceA I, Bbv I, BciV I, BpuE I, BseM II, BseR I, Bsg I,BsmF I, BtgZ I, Eci I, Eco57M I, Fok I, Hga I, Hph I, Mbo II, Mnl I,SfaN I, TspDT I, TspDW I, Taq II, and the like. In some exemplaryembodiments, the Type IIs restriction endonucleases used in the presentinvention are AcuI, which has a cut length of about 16 bases with a2-base 3′ overhang and the Type III endonuclease EcoP15, which has a cutlength of about 25 bases with a 2-base 5′ overhang. As will be discussedfurther below, the inclusion of a Type IIs and Type III sites in theadaptors of the nucleic acid template constructs of the invention is onetool for inserting multiple adaptors in a target nucleic acid at adefined location.

As will be appreciated, adaptors may also comprise other elements,including recognition sites for other (non-Type IIs) restrictionendonucleases, primer binding sites for amplification as well as bindingsites for probes used in sequencing reactions (“anchor probes”),described further herein. Adaptors of use in the invention may inaddition contain palindromic sequences, which can serve to promoteintramolecular binding once nucleic acid templates comprising suchadaptors are used to generate concatemers, as is discussed in moredetail below.

Control over the spacing and orientation of insertion of each subsequentadaptor provides a number of advantages over random insertion ofinterspersed adaptors. In particular, the methods described hereinimprove the efficiency of the adaptor insertion process, thus reducingthe need to introduce amplification steps as each subsequent adaptor isinserted. In addition, controlling the spacing and orientation of eachadded adaptor ensures that the restriction endonuclease recognitionsites that are generally included in each adaptor are positioned toallow subsequent cleavage and ligation steps to occur at the properpoint in the nucleic acid construct, thus further increasing efficiencyof the process by reducing or eliminating the formation of nucleic acidtemplates that have adaptors in the improper location or orientation. Inaddition, control over location and orientation of each subsequentlyadded adaptor can be beneficial to certain uses of the resultant nucleicacid construct, because the adaptors serve a variety of functions insequencing applications, including serving as a reference point of knownsequence to aid in identifying the relative spatial location of basesidentified at certain positions within the target nucleic acid. Suchuses of adaptors in sequencing applications are described furtherherein.

The 5′ and 3′ ends of the double stranded fragments can optionally beadjusted, as described above. For example, many techniques used tofractionate nucleic acids result in a combination of lengths andchemistries on the termini of the fragments. For example, the terminimay contain overlaps, and for many purposes, blunt ends of the doublestranded fragments are preferred. This can be done using knowntechniques such as a polymerase and dNTPs. Similarly, the fractionationtechniques may also result in a variety of termini, such as 3′ and 5′hydroxyl groups and/or 3′ and 5′ phosphate groups. In some embodiments,as described below, it is desirable to enzymatically alter thesetermini. For example, to prevent the ligation of multiple fragmentswithout the adaptors, it can be desirable to alter the chemistry of thetermini such that the correct orientation of phosphate and hydroxylgroups is not present, thus preventing “polymerization” of the targetsequences. The control over the chemistry of the termini can be providedusing methods known in the art. For example, in some circumstances, theuse of phosphatase eliminates all the phosphate groups, such that allends contain hydroxyl groups. Each end can then be selectively alteredto allow ligation between the desired components.

In addition, as needed, amplification can also optionally be conductedusing a wide variety of known techniques to increase the number ofgenomic fragments for further manipulation, although in manyembodiments, an amplification step is not needed at this step.

In some embodiments, if amplification is used to increase the number offragments before or after any steps of constructing the nucleic acidtemplate, that amplification is an MDA reaction using one or more of theadditives described above to reduce bias that could otherwise resultfrom the amplification.

After fractionation and optional termini adjustment, a set of adaptor“arms” are added to the termini of the genomic fragments. The twoadaptor arms, when ligated together, form the first adaptor. Forexample, as depicted in FIG. 6, circularization (605) of a linearconstruct with an adaptor arm on each end of the construct ligates thetwo arms together to form the full adaptor (606) as well as the circularconstruct (607). Thus, a first adaptor arm (603) of a first adaptor isadded to one terminus of the genomic fragment, and a second adaptor arm(604) of a first adaptor is added to the other terminus of the genomicfragment. Generally, and as more fully described below, either or bothof the adaptor arms will include a recognition site for a Type IIsendonuclease, depending on the desired system. Alternatively, theadaptor arms can each contain a partial recognition site that isreconstituted upon ligation of the arms.

In order to ligate subsequent adaptors in a desired position andorientation for sequencing, the present invention provides a method inwhich a Type IIs restriction endonuclease binds to a recognition sitewithin the first adaptor of a circular nucleic acid construct and thencleaves at a point outside the first adaptor and in the genomic fragment(also referred to herein as the “target nucleic acid”). A second adaptorcan then be ligated into the point at which cleavage occurs (again,usually by adding two adaptor arms of the second adaptor). In order tocleave the target nucleic acid at a known point, it can be desirable toblock any other recognition sites for that same enzyme that may randomlybe encompassed in the target nucleic acid, such that the only point atwhich that restriction endonuclease can bind is within the firstadaptor, thus avoiding undesired cleavage of the constructs. Generally,the recognition site in the first adaptor is first protected frominactivation, and then any other unprotected recognition sites in theconstruct are inactivated, generally through methylation. That is,methylated recognition sites will not bind the enzyme, and thus nocleavage will occur. Only the unmethylated recognition site within theadaptor will allow binding of the enzyme with subsequent cleaving.

One method of protecting the recognition site in the first adaptor frominactivation is to make the site single stranded, as the methylationenzyme will not bind to a single strand. Thus, one method of protectingthe recognition site of the first adaptor is by amplifying the lineargenomic fragments ligated to the two first adaptor arms using primersmodified with uracil. The primers are complementary to the adaptor armsand are modified with uracil such that, upon amplification (generallyusing PCR), the resultant linear constructs contain uracil embedded inthe recognition site of one of the first adaptor arms. Digestion of theuracil using known techniques renders that first adaptor arm (orwhatever contains the uracil) single stranded. A sequence specificmethylase is then applied to the linear constructs that will methylateall of the double-stranded recognition sites for the same endonucleaseas that contained in the first adaptor. Such a sequence-specificmethylase will not be able to methylate the single stranded recognitionsite in the first adaptor arm, and thus the recognition site in thefirst adaptor arm will be protected from inactivation by methylation. Asdescribed below, if a restriction site is methylated, it will not becleaved by the restriction endonuclease enzyme.

In some cases, as more fully described below, a single adaptor may havetwo of the same recognition sites, to allow cleavage both “upstream” and“downstream” from the same adaptor. In this embodiment, as depicted inFIG. 7, the primers and uracil positions are chosen appropriately, suchthat either the “upstream” or “downstream” recognition site may beselectively protected from inactivation or inactivated. For example, inFIG. 7, the two different adaptor arms (represented as rectangles) eachcomprise a recognition site for a restriction endonuclease (representedby the circle in one adaptor arm and by a triangle in the other). If theadaptor arm with the recognition site represented by the circle needs tobe protected using the above-described uracil degradation method, thenthe uracil-modified amplification primers are designed to incorporateuracils into that recognition site. Then upon uracil degradation, thatadaptor arm is rendered single stranded (represented by thehalf-rectangles), thus protecting that recognition site frominactivation.

After protecting the recognition site in the first adaptor arm frommethylation, the linear construct is circularized, for example, by usinga bridge oligonucleotide and T4 ligase. The circularizationreconstitutes the double stranded restriction endonuclease recognitionsite in the first adaptor arm. In some embodiments, the bridgeoligonucleotide has a blocked end, which results in the bridgingoligonucleotide serving to allow circularization, ligating thenon-blocked end, and leaving a nick near the recognition site. This nickcan be further exploited as discussed below. Application of therestriction endonuclease produces a second linear construct thatcomprises the first adaptor in the interior of the target nucleic acidand termini comprising (depending on the enzyme) a two base overhang.

A second set of adaptor arms for a second adaptor is ligated to thesecond linear construct. In some cases, when a nick is utilized, inorder to ensure that the adaptors are ligated in the proper orientation,the nick in the first adaptor is “translated” (or “translocated”) byusing a polymerase with exonuclease activity. The exonuclease activityof the polymerase (such as Taq polymerase) will excise the short DNAstrand that abuts the nick while the polymerase activity will “fill in”the nick and subsequent nucleotides in that strand (essentially, the Taqmoves along the strand, excising bases using the exonuclease activityand adding the same bases, with the result being that the nick istranslocated along the strand until the enzyme reaches the end).

In addition, to create an asymmetry of the template, one termini of theconstruct is modified with a single base. For example, certainpolymerases, such as Taq, will undergo untemplated nucleotide additionto result in addition of a single nucleotide to the 3′ end of the bluntDNA duplex, resulting in a 3′ overhang. As will be appreciated by thosein the art, any base can be added, depending on the dNTP concentrationin the solution. In certain embodiments, the polymerase utilized willonly be able to add a single nucleotide. For example, Taq polymerasewill be able to add a single G or A. Other polymerases may also be usedto add other nucleotides to produce the overhang. In one embodiment, anexcess of dGTP is used, resulting in the untemplated addition of aguanosine at the 3′ end of one of the strands. This “G-tail” on the 3′end of the second linear construct results in an asymmetry of thetermini, and thus will ligate to a second adaptor arm, which will have aC-tail that will allow the second adaptor arm to anneal to the 3′ end ofthe second linear construct. The adaptor arm meant to ligate to the 5′end will have a C-tail positioned such that it will ligate to the 5′G-tail. After ligation of the second adaptor arms, the construct iscircularized to produce a second circular construct comprising twoadaptors. The second adaptor will generally contain a recognition sitefor a Type IIs endonuclease, and this recognition site may be the sameor different than the recognition site contained in the first adaptor,with the latter finding use in a variety of applications

A third adaptor can be inserted on the other side of the first adaptorby cutting with a restriction endonuclease bound to a recognition sitein the second arm of the first adaptor (the recognition site that wasoriginally inactivated by methylation). In order to make thisrecognition site available, uracil-modified primers complementary to thesecond recognition site in the first adaptor are used to amplify thecircular constructs to produce third linear constructs in which thefirst adaptor comprises uracils embedded in the second restrictionrecognition site. The uracils are degraded to render the first adaptorsingle stranded, which protects the recognition site in the adaptor frommethylation. Applying a sequence-specific methylase will then inactivateall unprotected recognition sites. Upon circularization the recognitionsite in the first adaptor is reconstituted, and applying the restrictionendonuclease will cleave the circle, producing a position at which thethird adaptor can be inserted in a third linear construct. Ligatingthird adaptor arms to the third linear construct will follow the samegeneral procedure described above—the third linear construct will be A-or G-tailed, the third adaptor arms will be T- or C-tailed, allowing theadaptor arms to anneal to the third linear construct and be ligated. Thelinear construct comprising the third adaptor arms is then circularizedto form a third circular construct. Like the second adaptor, the thirdadaptor will generally comprise a recognition site for a restrictionendonuclease that is different than the recognition site contained inthe first adaptor.

A fourth adaptor can be added by utilizing Type IIs restrictionendonucleases that have recognition sites in the second and thirdadaptors. Cleavage with these restriction endonucleases will result in afourth linear construct that can then be ligated to fourth adaptor arms.Circularization of the fourth linear construct ligated to the fourthadaptor arms will produce the nucleic acid template constructs of theinvention. As will be appreciated by those in the art, other adaptorscan be added. Thus, the methods described herein allow two or moreadaptors to be added in an orientation and sometimes distance dependentmanner.

The present invention also provides methods for controlling theorientation in which each subsequently added adaptor is inserted. Such“nick translation” methods provide a way to control the way targetnucleic acids and adaptors ligate to each other. These methods alsoprevent artifacts in the nucleic acid constructs by preventing ligationof adaptors to other adaptors and target nucleic acid molecules to othertarget nucleic acid molecules (essentially avoiding the “polymerization”of adaptors and target nucleic acid molecules). Examples of differentorientations in which adaptors and target nucleic acid molecules can beligated are schematically illustrated in FIG. 8. Target nucleic acids801 and 802 are preferably ligated to adaptors 803 and 804 in a desiredorientation (as illustrated in this FIG., the desired orientation is onein which the ends with the same shape—circle or square—ligates to eachother). Modifying the ends of the molecules avoids the undesiredconfigurations 807, 808, 809 and 810, in which the target nucleic acidsligate to each other and the adaptors ligate to each other. In addition,as will be discussed in further detail below, the orientation of eachadaptor-target nucleic acid ligation can also be controlled throughcontrol of the chemistry of the termini of both the adaptors and thetarget nucleic acids. The control over the chemistry of the termini canbe provided using methods known in the art. For example, in somecircumstances, the use of phosphatase eliminates all the phosphategroups, such that all ends contain hydroxyl groups. Each end can then beselectively altered to allow ligation between the desired components.These and other methods for modifying ends and controlling insertion ofadaptors in the nick translation methods of the invention are describedin further detail below.

These nucleic acid template constructs (“monomers” comprising targetsequences interspersed with these adaptors) can then be used in thegeneration of concatemers, which in turn form the nucleic acid nanoballsthat can be used in downstream applications, such as sequencing anddetection of specific target sequences.

The present invention provides methods for forming nucleic acid templateconstructs comprising multiple interspersed adaptors inserted into atarget nucleic acid. As discussed further herein, methods of theinvention allow insertion of each subsequent adaptor by utilizingrecognition sites for Type IIs restriction endonucleases that areincluded in the adaptors. In order to insert multiple adaptors in adesired order and/or orientation, it can be necessary to blockrestriction endonuclease recognition sites contained within the targetnucleic acids, such that only the recognition site in the adaptor isavailable for binding the enzyme and the subsequent cleavage. Among theadvantages of such methods is that the same restriction endonucleasesite can be used in each adaptor, which simplifies production ofcircular templates that will eventually be used to generate concatemers,adaptors can be inserted using a previously inserted adaptor as a“stepping stone” for the next, such that addition can occur in effect by“walking” down the length of the fragment with each new adaptor.Controlling the recognition sites available for restriction enzymes alsoavoids the excision of certain sequences, thereby obtaining only limitedsequence representation (which could result if sites within the targetnucleic acid were accessible).

II.D.2. Addition of First Adaptor

As a first step in the creation of nucleic acid templates of theinvention, a first adaptor is ligated to a target nucleic acid. Theentire first adaptor may be added to one terminus, or two portions ofthe first adaptor, referred to herein as “adaptor arms”, can be ligatedto each terminus of the target nucleic acid. The first adaptor arms aredesigned such that upon ligation they reconstitute the entire firstadaptor. As described further above, the first adaptor will generallycomprise one or more recognition sites for a Type IIs restrictionendonuclease. In some embodiments, a Type IIs restriction endonucleaserecognition site will be split between the two adaptor arms, such thatthe site is only available for binding to a restriction endonucleaseupon ligation of the two adaptor arms.

FIG. 6 is a schematic representation of one aspect of a method forassembling adaptor/target nucleic acid templates (also referred toherein as “target library constructs”, “library constructs” and allgrammatical equivalents). DNA, such as genomic DNA 601, is isolated andfragmented into target nucleic acids 602 using standard techniques asdescribed above. The fragmented target nucleic acids 602 are thenrepaired so that the 5′ and 3′ ends of each strand are flush or bluntended. Following this reaction, each fragment is “A-tailed” with asingle A added to the 3′ end of each strand of the fragmented targetnucleic acids using a non-proofreading polymerase. The A-tailing isgenerally accomplished by using a polymerase (such as Taq polymerase)and providing only adenosine nucleotides, such that the polymerase isforced to add one or more A's to the end of the target nucleic acid in atemplate-sequence-independent manner.

In the exemplary method illustrated in FIG. 6, a first (603) and secondarm (603) of a first adaptor is then ligated to each target nucleicacid, producing a target nucleic acid with adaptor arms ligated to eachend. In one embodiment, the adaptor arms are “T tailed” to becomplementary to the A tails of the target nucleic acid, facilitatingligation of the adaptor arms to the target nucleic acid by providing away for the adaptor arms to first anneal to the target nucleic acids andthen applying a ligase to join the adaptor arms to the target nucleicacid.

In a further embodiment, the invention provides adaptor ligation to eachfragment in a manner that minimizes the creation of intra- orintermolecular ligation artifacts. This is desirable because randomfragments of target nucleic acids forming ligation artifacts with oneanother create false proximal genomic relationships between targetnucleic acid fragments, complicating the sequence alignment process.Using both A tailing and T tailing to attach the adaptor to the DNAfragments prevents random intra- or inter-molecular associations ofadaptors and fragments, which reduces artifacts that would be createdfrom self-ligation, adaptor-adaptor or fragment-fragment ligation.

As an alternative to A/T tailing (or G/C tailing), various other methodscan be implemented to prevent formation of ligation artifacts of thetarget nucleic acids and the adaptors, as well as orient the adaptorarms with respect to the target nucleic acids, including usingcomplementary NN overhangs in the target nucleic acids and the adaptorarms, or employing blunt end ligation with an appropriate target nucleicacid to adaptor ratio to optimize single fragment nucleic acid/adaptorarm ligation ratios.

After creating a linear construct comprising a target nucleic acid andwith an adaptor arm on each terminus, the linear target nucleic acid iscircularized (605), a process that will be discussed in further detailherein, resulting in a circular construct 607 comprising target nucleicacid and an adaptor. Note that the circularization process results inbringing the first and second arms of the first adaptor together to forma contiguous first adaptor (606) in the circular construct. In someembodiments, the circular construct 607 is amplified, such as by circledependent amplification, using, e.g., random hexamers and φ29 orhelicase. Alternatively, target nucleic acid/adaptor structure mayremain linear, and amplification may be accomplished by PCR primed fromsites in the adaptor arms. The amplification preferably is a controlledamplification process and uses a high fidelity, proof-readingpolymerase, resulting in a sequence-accurate library of amplified targetnucleic acid/adaptor constructs where there is sufficient representationof the genome or one or more portions of the genome being queried.

II.D.3. Addition of Multiple Adaptors

As discussed above, FIG. 6 is a schematic representation of one aspectof a method for assembling adaptor/target nucleic acid templates (alsoreferred to herein as “target library constructs”, “library constructs”and all grammatical equivalents). DNA, such as genomic DNA 601, isisolated and fragmented into target nucleic acids 102 using standardtechniques. The fragmented target nucleic acids 602 are then in someembodiments (as described herein) repaired so that the 5′ and 3′ ends ofeach strand are flush or blunt ended.

In the exemplary method illustrated in FIG. 6, a first (603) and secondarm (604) of a first adaptor is ligated to each target nucleic acid,producing a target nucleic acid with adaptor arms ligated to each end.

After creating a linear construct comprising a target nucleic acid andwith an adaptor arm on each terminus, the linear target nucleic acid iscircularized (605), a process that will be discussed in further detailherein, resulting in a circular construct 607 comprising target nucleicacid and an adaptor. Note that the circularization process results inbringing the first and second arms of the first adaptor together to forma contiguous first adaptor (606) in the circular construct. In someembodiments, the circular construct 607 is amplified, such as by circledependent amplification, using, e.g., random hexamers and φ29 orhelicase. Alternatively, target nucleic acid/adaptor structure mayremain linear, and amplification may be accomplished by PCR primed fromsites in the adaptor arms. The amplification preferably is a controlledamplification process and uses a high fidelity, proof-readingpolymerase, resulting in a sequence-accurate library of amplified targetnucleic acid/adaptor constructs where there is sufficient representationof the genome or one or more portions of the genome being queried.

Similar to the process for adding the first adaptor, a second set ofadaptor arms (610) and (611) can be added to each end of the linearmolecule (609) and then ligated (612) to form the full adaptor (614) andcircular molecule (613). Again, a third adaptor can be added to theother side of adaptor (609) by utilizing a Type IIs endonuclease thatcleaves on the other side of adaptor (609) and then ligating a third setof adaptor arms (617) and (618) to each terminus of the linearizedmolecule. Finally, a fourth adaptor can be added by again cleaving thecircular construct and adding a fourth set of adaptor arms to thelinearized construct. The embodiment pictured in FIG. 6 is a method inwhich Type IIs endonucleases with recognition sites in adaptors (620)and (614) are applied to cleave the circular construct. The recognitionsites in adaptors (620) and (614) may be identical or different.Similarly, the recognition sites in all of the adaptors illustrated inFIG. 6 may be identical or different.

As generally illustrated in FIG. 9, a circular construct comprising afirst adaptor may contain two Type IIs restriction endonucleaserecognition sites in that adaptor, positioned such that the targetnucleic acid outside the recognition sequence (and outside of theadaptor) is cut (910). The arrows around structure 510 indicate therecognition sites and the site of restriction. In process 911, EcoP15, aType IIs restriction endonuclease, is used to cut the circularconstruct. Note that in the aspect shown in FIG. 9, a portion of eachlibrary construct mapping to a portion of the target nucleic acid willbe cut away from the construct (the portion of the target nucleic acidbetween the arrow heads in structure 910). Restriction of the libraryconstructs with EcoP15 in process 911 results in a library of linearconstructs containing the first adaptor, with the first adaptor“interior” to the ends of the linear construct 912. The resulting linearlibrary construct will have a size defined by the distance between theendonuclease recognition sites and the endonuclease restriction siteplus the size of the adaptor. In process 913, the linear construct 912,like the fragmented target nucleic acid 904, is treated by conventionalmethods to become blunt or flush ended, A tails comprising a single Aare added to the 3′ ends of the linear library construct using anon-proofreading polymerase and first and second arms of a secondadaptor are ligated to ends of the linearized library construct by A-Ttailing and ligation 913. The resulting library construct comprises thestructure seen at 914, with the first adaptor interior to the ends ofthe linear construct, with target nucleic acid flanked on one end by thefirst adaptor, and on the other end by either the first or second arm ofthe second adaptor.

In process 915, the double-stranded linear library constructs aretreated so as to become single-stranded 916, and the single-strandedlibrary constructs 916 are then ligated 917 to form single-strandedcircles of target nucleic acid interspersed with two adaptors 918. Theligation/circularization process of 917 is performed under conditionsthat optimize intramolecular ligation. At certain concentrations andreaction conditions, the local intramolecular ligation of the ends ofeach nucleic acid construct is favored over ligation between molecules.

II.D.4. Controlling Orientation of Ligation Between Target Nucleic Acidsand Adaptors

In one aspect, the present invention provides methods in which ligationof adaptors to target nucleic acids, as described above, is accomplishedin a desired orientation. Such control over orientation is advantageous,because random fragments of target nucleic acids forming ligationartifacts with one another create false proximal genomic relationshipsbetween target nucleic acid fragments, complicating the sequencealignment process.

There are several methods that find use in controlling orientation ofthe adaptor insertion. As described above, altering the chemistry of thetermini of the targets and the adaptors can be done, such that ligationcan only occur when the correct orientation is present. Alternatively,“nick translation methods” can be done, which also rely on the terminichemistries, as outlined below. Finally, methods involving amplificationwith specific choices of primers can be done as described below.

FIG. 12 is a schematic illustration of the different orientations inwhich a second adaptor may be added to a nucleic acid construct. Again,process 1200 begins with circular library construct 1202, having aninserted first adaptor 1210. First adaptor 1210 has a specificorientation, with a rectangle identifying the “outer strand” of thefirst adaptor and a diamond identifying the “inner strand” of the firstadaptor (Ad1 orientation 1210). A Type IIs restriction endonuclease sitein the first adaptor 1210 is indicated by the tail of arrow 1201, andthe site of cutting is indicated by the arrow head. Process 1203comprises cutting with the Type IIs restriction endonuclease, ligatingfirst and second adaptor arms of a second adaptor, andrecircularization. As can be seen in the resulting library constructs1204 and 1206, the second adaptor can be inserted in two different waysrelative to the first adaptor. In the desired orientation 1204, the ovalis inserted into the outer strand with the rectangle, and the bowtie isinserted into the inner strand with the diamond (Ad2 orientation 1220).In the undesired orientation the oval is inserted into the inner strandwith the diamond and the bowtie is inserted into the outer strand withthe rectangle (Ad2 orientation 1230).

Although much of the following discussion and referenced illustrativefigures discuss for clarity's sake insertion of a second adaptor inrelation to a first, it will be appreciated that the processes discussedherein are applicable to adaptors added subsequently to the secondadaptor, creating library constructs with three, four, five, six, seven,eight, nine, ten or more inserted adaptors.

In one embodiment, both A tailing and T tailing are used to attach anadaptor to a nucleic acid fragment. For example, following themodifications described above to repair the ends of fragments, eachfragment can be “A-tailed” with a single A added to the 3′ end of eachstrand of the fragmented target nucleic acids using a non-proofreadingpolymerase. The A-tailing is generally accomplished by using apolymerase (such as Taq polymerase) and providing either only adenosinenucleotides (or an excess thereof), such that the polymerase is forcedto add one or more A's to the end of the target nucleic acid in atemplate-sequence-independent manner. In embodiments in which“A-tailing” is used, ligation to adaptor (or adaptor arms) can beaccomplished by adding a “T-tail” to the 5′ end of the adaptor/adaptorarms to be complementary to the A tails of the target nucleic acid,facilitating ligation of the adaptor arms to the target nucleic acid byproviding a way for the adaptor arms to first anneal to the targetnucleic acids and then applying a ligase to join the adaptor arms to thetarget nucleic acid.

Because the aspects of the claimed invention work optimally when nucleicacid templates are of a desired size and comprise target nucleic acidderived from a single fragment, it can be beneficial to ensure thatthroughout the process of producing nucleic acid templates that thecircularization reactions occur intramolecularly. That is, it can bebeneficial to ensure that target nucleic acids in the process of beingligated to a first, second, third, etc. adaptor do not ligate to oneanother. One embodiment of controlling the circularization process isillustrated in FIG. 10. As shown in FIG. 10, blocking oligos 1017 and1027 are used to block the binding regions 1012 and 1022 regions,respectively. Blocker oligonucleotide 1017 is complementary to bindingsequence 1016, and blocker oligonucleotide 1027 is complementary tobinding sequence 1026. In the schematic illustrations of the 5′ adaptorarm and the 3′ adaptor arm, the underlined bases are dideoxycytosine(ddC) and the bolded font bases are phosphorylated. Blockeroligonucleotides 1017 and 1027 are not covalently bound to the adaptorarms, and can be “melted off” after ligation of the adaptor arms to thelibrary construct and before circularization; further, the dideoxynucleotide (here, ddC or alternatively a different non-ligatablenucleotide) prevents ligation of blocker to adaptor. In addition or asan alternative, in some aspects, the blocker oligo-adaptor arm hybridscontain a one or more base gap between the adaptor arm and the blockerto reduce ligation of blocker to adaptor. In some aspects, theblocker/binding region hybrids have T_(m)s of about 37° C. to enableeasy melting of the blocker sequences prior ligation of the adaptor arms(circularization).

II.D.5. Controlling Orientation of Ligation: Arm-by-Arm Ligation

In one aspect, the directional insertion of adaptors can be controlledwithout modifying the termini of the target nucleic acid using an“arm-by-arm” ligation method. In general, this is a two-step ligationprocess in which an adaptor arm is added to a target nucleic acid andprimer extension with strand displacement produces two double strandedmolecules each with an adaptor arm on one end—a second adaptor arm canthen be ligated to the terminus without an adaptor arm. This process canprevent the creation of nucleic acid molecules that comprise the sameadaptor arm on both termini—for example, as depicted in FIG. 11A, thearm-by-arm ligation process can prevent the formation of nucleic acidmolecules that have both termini occupied by Adaptor A or Adaptor B. Inmany embodiments it is preferred that each terminus of a target nucleicacid is ligated to a different adaptor arm, such that when the two armsare ligated they are able to form a complete whole adaptor. This can beparticularly useful for minimizing the number of amplification stepsthat are needed after addition of each adaptor arm, because thearm-by-arm ligation reduces the number of non-useful molecules producedin each ligation reaction.

FIG. 11 illustrates one embodiment of the arm-by-arm ligation method. Inthis embodiment, one strand of the first adaptor arm A is added to bothstrands of a dephosphorylated target nucleic acid. This adaptor arm isblocked on one end (depicted as the closed circle), generally by usingalkaline phosphatase. Primer exchange can be used to replace the strandwith the blocked end. Primer extension with strand displacement (whichcan be accomplished, in one exemplary embodiment, through the use of φ29or Pfu polymerase) will prime from both ends and extend through thewhole insert, resulting in two double-stranded nucleic acid molecules,each with an adaptor arm A on one terminus and a blunt end on the other.In an alternative embodiment, adaptor arm A can be used pre-hybridizedwith a primer upstream of the blocked strand to initiate primerextension without requiring a primer exchange reaction. After thestrand-displacing polymerase reaction, a second adaptor arm B can thenbe ligated, generally to the blunt end of the target nucleic acid ratherthan to the terminus with the adaptor arm. This arm-by-arm ligationprocess can prevent the formation of target nucleic acids that comprisethe same adaptor arm on both termini.

II.D.6. Controlling Orientation of Ligation: Nick Translation Methods

In one embodiment, the present invention provides “nick translationmethods” for constructing nucleic acid molecules. In one embodiment,nick translation methods are used to ligate nucleic acid molecules in adesired orientation. In a further embodiment, nick translation methodsare used for inserting adaptors in a desired orientation. Such methodsgenerally involve modifying one or both termini of one or both of thenucleic acid molecules to be ligated together. For example, whenligating an adaptor to a target nucleic acid, one or both termini ofeither or both the target nucleic acid and adaptor to be ligated aremodified. Following such modification, a “translocation” or“translation” of a nick inserted into one strand of a construct providesthe ability to control the final orientation of the ligatedadaptor-target nucleic acid construct. “Nick translation methods” asdescribed herein may also include primer extension or gap-fill-inmethods, as is described in further detail below. Although the followingdiscussion is provided in terms of controlling ligation of adaptors totarget nucleic acids, it will be appreciated that these methods are notlimited to ligation of adaptors and target nucleic acids, and that thesemethods can also be used to control ligation of any two nucleic acidmolecules. For example, nick translation methods and any othercontrolled ligation methods described herein can be used as part ofgenetic and/or DNA engineering methods, such as the construction of newplasmids or other DNA vectors, gene or genome synthesis ormodifications, as well as in constructing building blocks fornanotechnology constructs.

FIG. 13 is a schematic illustration of such a “nick translation” type ofprocess. Construct 1306 in FIG. 13 is formed using methods discussedherein, and has an interspersed adaptor 1304, with a restrictionendonuclease recognition site (tail of the arrow in FIG. 13), and acleavage site. In FIG. 14, the library construct is not circularized,but is a branched concatemer of alternating target nucleic acidfragments 1406 (with restriction endonuclease recognition sites 1404)and adaptors 1412; however, the nick translation type process shown inFIG. 13 may be performed on such a library construct configuration aswell. The term “library construct” as used herein refers to nucleic acidconstructs comprising one or more adaptors, and is interchangeable withthe term “nucleic acid template”.

The library constructs with an inserted first adaptor are digested by arestriction endonuclease (process 1301)—in certain aspects, a Type IIsrestriction endonuclease—that cuts the target nucleic acid to render 3′nucleotide overhangs 1308. In FIG. 13, two nucleotides (NN-3′) 1308 areshown, though the number of overhanging nucleotides varies inalternative aspects depending at least in part on the identify of therestriction endonuclease used. The library construct 1310 is linearized,with the first inserted adaptor shown at 1304. The first insertedadaptor 1304 is engineered such that it comprises either a nick 1312 atthe boundary of the adaptor fragment or it comprises the recognitionsite for a nicking endonuclease that permits the introduction of a nick1314 at the interior of the adaptor. In either case, library construct1310 is treated 1303 with a polymerase 1316 that can extend the upperstrand from nick 1312 or 1314 to the end of the lower strand of libraryconstruct 1310 to form a strand having a 3′ overhang at one end and ablunt end at the other. To this library construct 1310, a second adaptor1318 is ligated in process 1305, where the second adaptor 1318 has adegenerate nucleotide overhang at one end and a single 3′ nucleotide(e.g., dT) overhang at the other end to form library construct 1320.Library construct 1320 is then treated (e.g., with Taq polymerase) inprocess 1307 to add a 3′ dA to the blunt end. Library construct 1322 maythen be amplified by PCR, with, e.g., uracil-containing primers.Alternatively, library construct 1322 may then be circularized inprocess 1309 in which case CDA may be performed (such as in step 1421 ofFIG. 14). Combining the processes discussed herein with the nicktranslation type process shown in FIG. 13 allows for selecting both therelative position and relative orientation of subsequently-addedadaptors to any adaptors previously inserted into the libraryconstructs.

In order to utilize a nick translation type of procedure, it may bebeneficial to modify one or both of the termini of the target nucleicacid and/or the adaptor as discussed above. In one exemplary embodiment,a first arm of an adaptor that is meant to ligate to the 3′ end of atarget nucleic acid may be designed such that its 3′ terminus isblocked, such that only the 5′ end of the adaptor arm is available toligate to only the 3′ end of the target nucleic acid. Similarly, thesecond arm that is meant to ligate to the 5′ end of the target nucleicacid may be designed such that its 5′ end is blocked, such that only the3′ end of the second arm can ligate to the 5′ end of the target nucleicacid. Methods for blocking one terminus of the adaptor arm and/or thetarget nucleic acid are well known in the art. For example, the targetnucleic acid (which is also referred to herein as a “nucleic acidinsert” or a “DNA insert” or an “insert”) is treated with enzymes thatgenerate defined functional ends and remove phosphates from both the 3′and 5′ ends as discussed above. Removing all of the phosphate groupsrenders the target nucleic acid molecules unable to ligate to eachother. Adaptors in this embodiment are also designed to have one strandcapable of ligation (for example by creating or maintaining a 5′phosphate group) and a complementary strand that has a 3′ end that isprotected from ligation. Generally, this protection of the 3′ end isaccomplished using a dideoxy nucleotide to inactivate the 3′ end. Thus,when the modified target nucleic acids lacking phosphate groups on bothends and modified adaptors comprising only a phosphate group on one 5′end with a 3′ block (for example, a dideoxy) on the complementarystrand, the only ligation product that will form is that of targetnucleic acid ligated to the 5′ end of the adaptor that has a phosphategroup. Subsequent to this ligation step, the protected 3′ end of theadaptor can be exchanged with a strand containing a functional 3′ end.This exchange is generally accomplished by taking advantage of the factthat the strand with 3′ protection is generally short and easy todenature. The exchange strand with a functional 3′ end is longer andwill thus bind more efficiently to the complementary strand—in furtherembodiments, the strand with the functional end is also added in higherconcentrations to further influence the reaction toward exchanging theprotected strand with the strand with the functional end. This strandwith the functional 3′ end is then primed by adding a DNA polymerasewith nick translation activity, such that the polymeraseexonucleolytically removes bases from the 5′ end of the target nucleicacid, thereby exposing a functional 5′ phosphate. This newly generated5′ phosphate can be ligated to the extension product by a ligase, (Ifligase is absent during the extension reaction, two polymerase moleculeswill nick translate from each end of the target nucleic acid until theymeet each other, resulting in a broken molecule). For example, asillustrated in FIG. 2, the target nucleic acid (insert) is firstend-repaired to form defined functional ends, preferentially blunt-ends.Next, to avoid concatemerization of inserts, 5′-end phosphates areremoved. The insert is then mixed with DNA ligase and DNA adaptors. TheDNA adaptor contains two oligonucleotides, and has one blunt-end and onesticky-end when the two oligonucleotides are hybridized together. Theblunt-end side contains one “top-strand” with a protected/inactivated3′-end, and one “bottom-strand” with a functional 5′-end phosphate, andare thus also unable to self-ligate. The only possible ligationcombination is therefore one insert with one “bottom-strand”blunt-ligated to each end. The “top-strand” with 3′-end protection isthen exchanged with an oligonucleotide containing a functional 3′-endthat can act as a primer in a polymerase extension reaction. Uponaddition of polymerase and ligase, the second oligonucleotide can bebuilt-in through a nick translation and ligation reaction. When thepolymerase is extending into the insert, it introduces a nick with afunctional 5′-end phosphate that can be recognized and sealed by DNAligase. The resulting insert with an adaptor or adaptor arm on each sideof each strand can now be subjected to PCR using primers specific to theadaptor.

Generally in a nick translation reaction such as the one describedabove, an active ligase is present or added in the mixture beforeaddition of the polymerase or simultaneously with the polymerase. Insome embodiments, it can be beneficial to use low activity polymerase(slow nick translation) conditions. Both addition of the ligase beforeor simultaneously with the polymerase and low activity conditions canhelp assure that the translating nick is sealed before reached theopposite end of the DNA fragment. In some embodiments, this can achievedby incubating the Taq polymerase with T4 ligase at 37° C., a temperaturethat will usually result in low polymerase activity and high ligaseactivity. The reaction may then be further incubated at a highertemperature (such as 50-60° C.) to further assurenick-translation-ligation occurs to completion across most/allconstructs in the reaction.

In further embodiments, the present invention provides methods forforming nucleic acid template constructs comprising multipleinterspersed adaptors. Methods of the present invention include methodsof inserting multiple adaptors such that each subsequent adaptor isinserted in a defined position with respect to one or more previouslyadded adaptors. Certain methods of inserting multiple interspersedadaptors are known in the art, for example, as discussed in U.S.Application Ser. Nos. 60/992,485; 61/026,337; 61/035,914; 61/061,134;61/116,193; 61/102,586; 12/265,593; 12/266,385; 11/679,124; 11/981,761;11/981,661; 11/981,605; 11/981,793 and 11/981,804, each of which isherein incorporated by reference in its entirety for all purposes and inparticular for all teachings related to methods and compositions forcreating nucleic acid templates comprising multiple interspersedadaptors as well as all methods for using such nucleic acid templates.Insertion of known adaptor sequences into target sequences, such thatthere is an interruption of contiguous target sequence with the multipleinterspersed adaptors, provides the ability to sequence both “upstream”and “downstream” of each adaptor, thus increasing the amount of sequenceinformation that can be generated from each nucleic acid template. Thepresent invention provides further methods for inserting each subsequentadaptor in a defined position with respect to one or more previouslyadded adaptors.

Nick translation ligation is usually performed after ligating the firststrand by adding at least polymerase to the reaction. In someembodiments, the nick translation reaction may be performed as aone-step reaction by adding all components at once, while in someembodiments the steps of the reaction are performed sequentially. Thereare multiple possible embodiments of a “one-step” approach of the nicktranslation reaction. For example, a single mix with a primer can beused in which Taq is added at the beginning of the reaction. Use of athermo-stable ligase provides the ability of performing primer exchangeand nick translation ligation (and PCR if necessary) by simplyincreasing the temperature. In another exemplary embodiment, thereaction mixture will contain a minimal concentration of non-processivenick-translating polymerase with a weak 3′ exonuclease that activatesthe 3′ blocked strand.

In a further embodiment, T4 polynucleotide kinase (PNK) or alkalinephosphatase is used to alter 3′ ends of adaptors and/or target nucleicacids to prepare them for a nick translation process. For example,adaptors can be inserted as part of a circularization reaction.End-repaired and alkaline phosphatase treated target nucleic acids areligated to adaptors, and in this exemplary embodiment are designed toform self-complementary hairpin shaped units (FIG. 16). The hairpins aredesigned to contain modifications at a given position that can berecognized and cleaved by enzymes or chemicals. For example, if thehairpins contain deoxyuridines, the deoxyuridiines can be recognized andcut by UDG/EndoVIII. After cutting, the two hairpins becomesingle-stranded with phosphates on their respective 3-end. These 3′phosphates can then be removed by either T4 Polynucleotide Kinase (PNK)or alkaline phosphatase (SAP) to enable nick-translation methods asdescribed further herein. In an exemplary embodiment such as the oneillustrated in FIG. 4A, the two hairpins are designed to be partlycomplementary to each other and can thus form, by intra-molecularhybridization, circularized molecules. Finally, the circularizedmolecules are subjected to a nick-translation process in which apolymerase extends into the insert and introduces a nick with afunctional 5′-end phosphate that can be recognized and sealed by DNAligase.

Instead of using hairpins as described above, a pair of double strandedadaptors that are partly complementary to each other can be used forcircularization. One pair has deoxyuridines on one strand that can berecognized and cut by UDG/EndoVIII. Other methods of nicking one strandcan also be used, including without limitation: nicking enzymes,incorporating inosine modified DNA that can be recognized byendonucleolytic enzymes, and incorporating DNA with RNA modificationsthat can be recognized by RNA-endonucleases. The target nucleic acid andadaptors can be prepared for controlled ligation as described above, forexample by treating the target nucleic acid with alkaline phosphatase tocreate blunt ends that are unable to ligate to other target nucleicacid. Circularization is activated by denaturing the short 3′-protectedstrand in the adaptor from the strand ligated to the target nucleicacid, leaving two partly complementary single stranded ends on each endof the target nucleic acid insert. The ends are then joined byintra-molecular hybridization and subjected to nick-translation andligation, forming a covalently closed circle. The circles are thentreated with UDG/EndoVIII to prepare the circle for directionalinsertion of the next adaptor.

In a still further embodiment illustrated in FIG. 15, a linear targetnucleic acid is treated with shrimp alkaline phosphatase (SAP) to remove5′ phosphates. Next, the target nucleic acid is ligated to one arm ofthe adaptor (arm A), containing a strand with a 5′ phosphate, and acomplementary shorter strand with a protected 3′ end. The ligationproduct is then subjected to nick-translation. The nick generated in thecircularization reaction is located on the top strand of the firstadaptor, and acts as a primer for the polymerase used in thenick-translation reaction. The polymerase extends the top-strand to thenick at the adaptor-insert junction, releasing one of the adaptor A armsand generating blunt end or A or G overhang. Next, the resultingpolymerase-generated insert end is ligated to the second adaptor arm(arm B). By designing the first adaptor to generate a nick in thecircularization reaction, the subsequent adaptor can be added in apredetermined orientation. This strategy is applicable for all type IIsrestriction enzymes or other enzymatic or non-enzymatic fragmentingmethods regardless of whether they generate a digested product that hasblunt ends, 3′ overhangs, or 5′ overhangs. A non-amplification optionmay also be used to close the circle comprising melting off the blockedoligonucleotides followed by DNA circularization via nick translationligation reaction.

Both proofreading polymerases (which have 3′-5′ exonuclease activity),such as Pfu polymerase, and non-proofreading polymerases (which lack3′-5′ exonuclease activity), such as Taq polymerase, can be used in thenick translation and strand synthesis with strand displacement processesdescribed herein. Proofreading polymerases can efficiently generateblunt-ends in the nick translation process but have the disadvantage ofalso degrading non-protected 3′ overhangs. The resulting nicktranslation product will therefore have two blunt ends and will thus beunable to ligate subsequent adaptors in defined orientation. Onesolution is to protect the 3′ end of the ligated adaptor (arm A in FIG.15 for example) from degradation, using e.g. dideoxyribonucleosidetriphosphates (ddNTP) on the 3′ ends. However, ddNTP protection alsoprotects the 3′ end from subsequent extension, thus limiting theadaptors to be carried forward in a direct circularization procedure.Another potential solution is to protect the 3′ ends from polymerasedegradation using modifications on the 3′ end (e.g. 3′ phosphate) thatcan be removed prior to nick translation circularization (e.g. usingalkaline phosphatase). Another approach is to use hairpin shapedadaptors (as described in FIG. 16) in combination with proofreadingpolymerase in nick translation reactions. These adaptors will beprotected from degradation but have the disadvantage of requiring anextra UDG/EndoVIII step. Furthermore, the inventors have found that oneof the proofreading polymerases, Pfu polymerase, is able to efficientlygenerate blunt ends without degrading the non-protected 3′ overhang,indicating a low 3′-5′ exonuclease activity.

Non-proofreading polymerases, such as Taq polymerase, can generate bothblunt ends and single base overhangs in the nick translation process(Taq can generate non-templated A- and G-tails in addition to bluntends). An advantage of using polymerases without 3′-5′ exonucleaseactivity in the nick translation process is that non-protected 3′overhangs remain intact. This enables ligation of subsequent adaptors indefined orientation without protecting 3′ overhangs from degradation. Apotential disadvantage with many proofreading polymerases is that theyhave a function of adding single nucleotides on 3′ ends in anon-templated process. This process can be hard to control, and willoften generate a mixed population of 3′ ends, resulting in a lowadaptor-to-insert ligation yield. In general, methods utilizing bluntend ligation are more efficient than one base overhang ligation.

In one embodiment, after ligation of a first adaptor, rather thanforming a circle and then cleaving with a type Ils endonuclease that hasa recognition site in the first adaptor (which is a step in someembodiments of producing nucleic acid templates of the invention, suchas embodiments schematically illustrated in FIGS. 6 and 9), a secondadaptor can be added using a variation of the nick translation method.Exemplary embodiments of this variation are schematically illustrated inFIG. 17. In general, these embodiments begin with addition of a firstadaptor to a target nucleic acid and then circularization, as isdescribed in detail above and illustrated in FIGS. 6 and 9. In theembodiment illustrated in FIG. 17A, a nick translation is carried outusing a polymerase with 5′-3′ exonuclease activity (such as Taqpolymerase), which generates an inverted circle with the first adaptorlocated in the interior of the target nucleic acid. This product canthen be end-repaired and subjected to ligation to adaptor 2 (usingmethods described in further detail above). One disadvantage of thisembodiment is that the target nucleic acid may be longer than isrequired for sequencing application, and such longer templates might beprone to generating secondary structures in any nucleic acid concatemerproducts generated from the templates (the generation of concatemersfrom nucleic acid templates of the invention is discussed in greaterdetail below). Such secondary structures may result in a decreasedsignal when these concatemers are used in sequencing applications, suchas the cPAL methods discussed below. One way to overcome thisdisadvantage is by shortening the target nucleic acid—one exemplaryembodiment of this approach is pictured in FIG. 17B. In this embodiment,the first adaptor is modified with uracils using methods describedherein. Following the nick translation-inversion of the circlecomprising the first adaptor, an adaptor C-arm is added to both ends ofthe end-repaired molecule. The uracil-modified adaptor 1 is treated toremove the uracils, creating gaps, and also treated to generateactivated 3′ ends. Generally, the uracils are removed by application ofan UDG/EndoVIII enzyme mix and PNK and/or alkaline phosphatase is usedto remove the 3′ phosphates and generate activated 3′ ends. Theactivated 3′ ends of the adaptor 1 and the 3′ ends of adaptor arm C arerecognized by a nick translation polymerase (i.e., a polymerase with5′-3′ exonuclease activity) resulting in a product with adaptor 1surrounded by a target nucleic acid that has been trimmed toapproximately half of its original length. This polymerase cuttingprocedure can be repeated to decrease the size of the target nucleicacid even further if adaptor 1 is modified with additional nickingmodifications (including without limitation incorporation of inosine,RNA-modifications, and the like).

In a further embodiment, as is illustrated in FIG. 17C, the nicktranslation methods illustrated in FIGS. 17A and B can be expanded toinsert multiple adaptors. By modifying adaptors, nicks or gaps andfunctional 3′ ends can be generated to prime nick translation reactionsfrom multiple adaptors simultaneously. As illustrated in FIG. 17C, anucleic acid construct comprising target nucleic acid and two adaptors,each containing a uracil modification on one strand, is circularized.Next, the circle is treated with an enzyme mix, such as UDG/EndoVIII, toremove the uracils and introduce gaps. These gaps can be simultaneouslynick translated to invert the circle, making the construct available forligation to additional adaptors. By adding multiple modifications on thesame adaptors, subsequent nicking/gapping and nick translation inversioncan be carried out to introduce multiple adaptors. In some embodiments,uracils can be added back to the same positions in the adaptors, makingthe adaptors suitable for further nick translation reactions. Adding theuracils back can be accomplished, for example, by incubating the nicktranslation reaction with uracil only to “build back” the modificationin the adaptor, followed by addition of non-modified nucleotides inhigher concentration to fill in the rest of the construct.

In a still further embodiment, illustrated in FIG. 17D, the targetnucleic acid may be trimmed by controlling the speed of the nicktranslation enzyme. For example, the nick translation enzyme can beslowed by altering the temperature or limiting reagents, which canresult in two nicks being introduced into the circularized insert thatare shifted from the initial sites in the adaptor using a nicktranslation process. Similarly, using a strand displacement polymerase(such as φ29) will result in a nick being shifted, producing a branchingpoint due to a displaced segment of the nucleic acid. These nick orbranch points can be recognized by various enzymes (including withoutlimitation S1 endonuclease, Bal31, T7 endonculease, Mung Beanendonuclease, as well as combinations of enzymes, such as a 5′ to 3′exonuclease such as T7 exonuclease and S1 or Mung Bean endonuclease)that will cut the opposite strand of the nick, resulting in a linearproduct. This product can then be end-repaired (if needed) and thenligated to the next adaptor. The size of the target nucleic acidremaining will be controlled by the speed of the nick translationreaction, again for example by lowering the concentration of reagentssuch as dNTPs or by conducting the reaction at a less than optimaltemperature. The size of the target nucleic acid may also be controlledby the incubation time of the nick translation reaction.

In a further embodiment, nick translation methods can be used to formnucleic acid templates without transitioning through any circularizingsteps. An exemplary embodiment of such methods is illustrated in FIG.18, which shows that the first adaptor 1801, which is shaped as ahairpin, is ligated to target nucleic acid 1802 using ligation methodsdescribed above, such as by treating the target nucleic acid with shrimpalkaline phosphate to remove phosphate groups and thereby control theends of the target nucleic acid that are available to ligate to thefirst adaptor. After ligation of the first adaptor, a controlleddouble-strand specific 5′-3′ exonuclease reaction is carried out togenerate single stranded 3′ ends. In some embodiments, the exonucleasereaction is carried out using a T7 exonuclease, although it will beappreciated that other double-strand specific exonucleases can be usedin this embodiment of the invention. In further embodiments, theexonuclease reaction generates single stranded 3′ ends of about 100 toabout 3000 bases in length. In still further embodiments, theexonuclease reaction generates single stranded 3′ ends of about 150 toabout 2500, about 200 to about 2000, about 250 to about 1500, about 300to about 1000, about 350 to about 900, about 400 to about 800, about 450to about 700, and about 500 to about 600 bases in length.

It will be appreciated that the nick translation processes describedherein can be used in combination with any of the other methods ofadding adaptors described herein. For example, the arm-by-arm ligationprocess described above and schematically illustrated in FIG. 11A can beused in combination with a nick translation process to prepare aconstruct for PCR amplification.

In a further embodiment, adaptor arm A used in an arm-by-arm ligationreaction can be designed for direct circularization without PCR,followed by nick translation ligation to seal the circle. In anexemplary embodiment, for direct circularization, adaptor arm A can bedesigned as pictured in FIG. 11B. Segment 1101 is designed to becomplementary to adaptor arm B. The construct in FIG. 11B allows fordirect primer extension by a strand displacing polymerase (such as φ29)without a need for a primer exchange reaction to remove a blocked end(the polymerase will not extend past the 3′ phosphate on segment 1102).This construct also provides a 3′ overhang for circularization. Segment1102 prevents hybridization of adaptor arm A to adaptor arm B beforecircularization. In some embodiments, segment 1102 may not be necessaryfor preventing hybridization to arm B (such as when adaptor arm B isprovided in very high concentrations) or segment 1102 may be part of thedesign of adaptor arm B rather than adaptor arm A.

After generating the single stranded 3′ ends, a second adaptor 1803 ishybridized to the single stranded 3′ end of the target nucleic acid andconnected to the first adaptor through a nick translation ligationreaction (in one embodiment, the nick translation ligation is a “primerextension” or “gap fill-in” reaction). The second adaptor has a 5′phosphate and a 3′ block (identified as the vertical line 1804). The 3′block can in some embodiments be a removable block such as a 3′phosphate, which can be removed in some exemplary embodiments usingpolynucleotide kinase (PNK) and/or shrimp alkaline phosphate. The secondadaptor may in some embodiments have degenerated bases at the 3′ and/orthe 5′ ends. In some exemplary embodiments, the second adaptor has about2-6 degenerated bases at the 5′ end and 4-9 degenerated bases at the 3′end, although it will be appreciated that any combination of numbers ofdegenerated bases at one or both ends of the second adaptor areencompassed by the present invention. In the embodiment pictured in FIG.18, the second adaptor comprises 3 degenerate bases at the 5′ end (“N3”)and 7 degenerate bases at its 3′ end (“N7”). The joining of the firstadaptor to the second adaptor may in some embodiments be accomplishedunder reaction conditions at which hybridization of the adaptors to thetarget nucleic acid are favored. In some exemplary embodiments, suchreaction conditions may include temperatures of from about 20 to about40° C. Polymerases that can be used under such reaction conditionsinclude without limitations φ29, Klenow, T4 polymerases and Pol I.

The ligation product 1805 is then denatured and/or further processedwith a 5′-3′ exonucleases followed by a re-annealing step to form twosingle stranded nucleic acid molecules (denoted by the “×2” in FIG. 18).During re-annealing, the N7 part of the second adaptor may hybridize toa segment at a random distance from the first hybridization sequencemotif, thereby forming a single stranded loop 1806. In some embodiments,the N7 end of the second adaptor may not hybridize until denaturationproduces long single stranded regions of the nucleic acid 1807. Theaverage distance between two captured genomic segments (which aregenerally from about 20 to about 200 bases in length) will in manyembodiments be between about 0.5 to about 20 kilobases. This averagedistance will depend in part on the number of degenerate bases (“Ns”) ofthe adaptors and the stringency of hybridization conditions. There-annealing step can then be followed by another round of adaptorhybridization and nick translation ligation. A final adaptor (in FIG.18, this final adaptor is pictured as a third adaptor 1808, but it willbe appreciated that the final adaptor may be the fourth, fifth, sixth,seventh or more adaptor inserted according to any of the methodsdescribed herein) is similar to the second adaptor but will in manyembodiments lack the degenerate bases at the 3′ end. In furtherembodiments, the final adaptor may comprise a binding site for a primerfor an amplification reaction, for example a PCR primer.

In still further embodiments, amplification reactions, such as PCRreactions (see 1809 in FIG. 18), can be carried out, for example, byusing primer binding sites included in the first and final adaptors. Instill further embodiments, the first and final adaptors may be two armsof the same adaptor and more than one adaptor may be inserted prior tothe addition of the final adaptor. In a yet further embodiment, theamplification products may be used to form circular double strandednucleic acid molecules for further adaptor insertion using any of theprocess described herein or known in the art.

II.D.7. Controlled Insertion of Subsequent Adaptors: Protection ofRestriction Endonuclease Recognition Sites

In addition to controlling the orientation of adaptors inserted into atarget nucleic acid as described above, multiple adaptors can also beinserted into a target nucleic acid at specified locations relative topreviously inserted adaptors. Such methods include embodiments in whichcertain restriction endonuclease recognition sites, particularlyrecognition sites contained in a previously inserted adaptor, areprotected from inactivation. In order to ligate subsequent adaptors in adesired position and orientation, the present invention provides methodsin which a Type IIs restriction endonuclease binds to a recognition sitewithin the first adaptor of a circular nucleic acid construct and thencleaves at a point outside the first adaptor and in the genomic fragment(also referred to herein as the “target nucleic acid”). A second adaptorcan then be ligated into the point at which cleavage occurs (again,usually by adding two adaptor arms of the second adaptor). In order tocleave the target nucleic acid at a known point, it is necessary toblock any other recognition sites for that same enzyme that may randomlybe encompassed in the target nucleic acid, such that the only point atwhich that restriction endonuclease can bind is within the firstadaptor, thus avoiding undesired cleavage of the constructs. Generally,the recognition site in the first adaptor is first protected frominactivation, and then any other unprotected recognition sites in theconstruct are inactivated, generally through methylation. By“inactivation” of a restriction endonuclease recognition site herein ismeant that the recognition site is somehow rendered unavailable forbinding by a restriction endonuclease, thus preventing the downstreamstep of cleavage by that enzyme. For example, methylated recognitionsites will not bind the restriction endonuclease, and thus no cleavagewill occur. Once all recognition sites in a nucleic acid construct thatare unprotected have been methylated, only the unmethylated recognitionsite within the adaptor will allow binding of the enzyme with subsequentcleaving. Other methods of inactivating recognition sites includewithout limitation applying a methylase block to the recognition site,using a blocking oligonucleotide to block the recognition site, usingsome other blocking molecule, such as a zinc finger protein, to blockthe recognition site, and nicking the recognition site to preventmethylation. Such methods for protecting the desired recognition siteare described in U.S. application Ser. Nos. 12/265,593, filed Nov. 5,2008 and 12/266,385, filed Nov. 6, 2008, which are both hereinincorporated by reference in their entirety and for all purposes and inparticular for all teachings related to inserting multiple interspersedadaptors into a target nucleic acid.

It will be appreciated that the methods described above for controllingthe orientation in which adaptors and target nucleic acids ligate toeach other may also be used in combination with the methods describedbelow for controlling the spacing of each subsequently added adaptor.

In one aspect, the present invention provides a method of protecting therecognition site in the first adaptor from inactivation by rendering therecognition site in the first adaptor single-stranded, such that amethylase that is only able to methylate double-stranded molecules willbe unable to methylate the recognition site being protected. One methodof rendering the recognition site in the first adaptor single-strandedis by amplifying the linear genomic fragments ligated to the two firstadaptor arms using primers modified with uracil. The primers arecomplementary to the adaptor arms and are modified with uracil suchthat, upon amplification (generally using PCR), the resultant linearconstructs contain uracil embedded in the recognition site of one of thefirst adaptor arms. The primers generate a PCR product with uracilsclose to the Type IIs restriction endonuclease recognition site in thefirst and/or second arms of the first adaptor. Digestion of the uracilrenders the region(s) of the adaptor arm that include the Type IIsrecognition site to be protected single stranded. A sequence specificmethylase is then applied to the linear constructs that will methylateall of the double-stranded recognition sites for the same endonucleaseas that contained in the first adaptor. Such a sequence-specificmethylase will not be able to methylate the single stranded recognitionsite in the first adaptor arm(s), and thus the recognition site in thefirst adaptor arm(s) will be protected from inactivation by methylation.

In some cases, as more fully described below, a single adaptor may havetwo of the same recognition sites, to allow cleavage both “upstream” and“downstream” from the same adaptor. In this embodiment, as depicted inFIG. 7, the primers and uracil positions are chosen appropriately, suchthat either the “upstream” or “downstream” recognition site may beselectively protected from inactivation or inactivated.

A third adaptor can be inserted on the other side of the first adaptorby cutting with a restriction endonuclease bound to a recognition sitein the second arm of the first adaptor (the recognition site that wasoriginally inactivated by methylation). In order to make thisrecognition site available, uracil-modified primers complementary to thesecond recognition site in the first adaptor are used to amplify thecircular constructs to produce third linear constructs in which thefirst adaptor comprises uracils embedded in the second restrictionrecognition site. The uracils are degraded to render the first adaptorsingle stranded, which protects the recognition site in the adaptor frommethylation. Applying a sequence-specific methylase will then inactivateall unprotected recognition sites. Upon circularization the recognitionsite in the first adaptor is reconstituted, and applying the restrictionendonuclease will cleave the circle, producing a position at which thethird adaptor can be inserted in a third linear construct. Ligatingthird adaptor arms to the third linear construct will follow the samegeneral procedure described above—the third linear construct will be A-or G-tailed, the third adaptor arms will be T- or C-tailed, allowing theadaptor arms to anneal to the third linear construct and be ligated. Thelinear construct comprising the third adaptor arms is then circularizedto form a third circular construct. Like the second adaptor, the thirdadaptor will generally comprise a recognition site for a restrictionendonuclease that is different than the recognition site contained inthe first adaptor.

A fourth adaptor can be added by utilizing Type IIs restrictionendonucleases that have recognition sites in the second and thirdadaptors. Cleavage with these restriction endonucleases will result in afourth linear construct that can then be ligated to fourth adaptor arms.Circularization of the fourth linear construct ligated to the fourthadaptor arms will produce the nucleic acid template constructs of theinvention.

In general, methods of the invention provide a way to specificallyprotect a Type IIs endonuclease recognition site from inactivation suchthat, once all remaining unprotected recognition sites in a constructare inactivated, application of the Type IIs endonuclease will result inbinding only to the protected site, thus providing control over wherethe subsequent cleavage occurs in the construct. The method describedabove provides one embodiment of how to protect the desired recognitionsite from inactivation. It will be appreciated that the above-describedmethod can be modified using techniques known in the art, and that suchmodified methods are encompassed by the present invention.

In one exemplary embodiment, each subsequently inserted adaptor isinserted using a method in which a recognition site is protected frominactivation using a combination of methods. FIG. 19 is a schematicillustration of an embodiment in which a second adaptor is inserted at adesired position relative to a first adaptor by employing a process thatis a combination of methylation and protection from methylation using acombination of uracil degradation and nickase. FIG. 19 shows genomic DNAof interest 1902 having a Type IIs restriction endonuclease recognitionsite at 1904. The genomic DNA is fractionated or fragmented in process1905 to produce fragment 1906 having a Type IIs restriction endonucleaserecognition site 1904. Adaptor arms 1908 and 1910 are ligated tofragment 1906 in process 1907. Fragment 1906 with first and secondadaptor arms 1908 and 1910 (a library construct) are amplified by PCR inprocess 1911, using uracil-modified primers 1912 complementary toadaptor arms 1908 and 1910. The primers generate a PCR product withuracils close to the Type IIs restriction endonuclease recognition site.In process 1913, the uracils are specifically degraded using, e.g.,uracil-DNA glycosylase enzyme (Krokan, et al., (1997) Biochem. J.325:1-16), leaving a PCR product that is single-stranded in the Type IIsrestriction endonuclease recognition site region. As shown, uracilincorporation and degradation may be used to render the Type IIsrestriction endonuclease recognition site single-stranded; however, asdescribed further herein, other methods may be employed to render theseregions single-stranded including use of 3′ or 5′ exonucleases in alimited digest.

In process 1915, a sequence-specific nickase is used to nick bases ineach double-stranded Type IIs restriction endonuclease recognition siteto protect these sites from Type IIs restriction endonucleaserecognition. However, the single-stranded Type IIs restrictionendonuclease recognition site portions in first and second adaptor arms1908 and 1910 will not be nicked, and, once circularized and ligated1917, the Type IIs restriction endonuclease recognition site in thefirst and second adaptor arms re-forms such that this Type IIsrestriction endonuclease recognition site is available for restriction.When selecting the nickase and the Type IIs restriction endonucleasesfor this process, it is preferred that the two enzymes recognize thesame sequence or that one enzyme recognizes a subsequence (sequencewithin the sequence) of the other enzyme. Alternatively, the nickase mayrecognize a different sequence, but is positioned within the adaptor sothat it nicks in the Type IIs restriction endonuclease recognition site.Use of uracil or 3′ or 5′ degradation permits the use of one nickaseenzyme throughout the process; alternatively, more than onesequence-specific nickase may be employed. The circularized construct isthen cut with the Type IIs restriction endonuclease in process 1919where the Type IIs restriction endonuclease recognition site isindicated at 1922, the construct is cut at 1920, and the nick isindicated at 1918, resulting in a linearized construct available forligation of a second set of adaptor arms to be added to the construct inprocess 1921

Ligation process 1921 adds first 1924 and second 1926 adaptor arms ofthe second adaptor to the linearized construct, and a secondamplification is performed by PCR at process 1923, again usinguracil-modified primers 1928 complementary to adaptor arms 1924 and1926. As before, the primers generate a PCR product with uracils closeto the Type IIs restriction endonuclease recognition site. In process1925, the uracils are specifically degraded leaving a PCR product thatis single-stranded in the Type IIs restriction endonuclease recognitionsite region of the first and second adaptor arms 1924 and 1926 of thesecond adaptor. Ligation process 1921 also serves to repair the nick1918 in the Type IIs restriction site 1904 in the target nucleic acidfragment 1906. In process 1927, the sequence-specific nickase again isused to nick bases in the double-stranded Type IIs restrictionendonuclease recognition sites in the target nucleic acid fragment(there is nicking 1914 of the Type IIs restriction endonucleaserecognition site 1904) and in the Type IIs restriction endonucleaserecognition site of the first adaptor 1930 protecting these sites fromType IIs restriction endonuclease recognition.

The nicked construct is then circularized and ligated at process 1929,where the Type IIs restriction endonuclease recognition site in thefirst and second arms 1924 and 1926 of the second adaptor is re-formed1932 and the process is repeated where the circularized construct is cutagain with the Type IIs restriction endonuclease in process 1931 togenerate another linearized construct (this one with first and secondadaptors already added) available for ligation of a third pair ofadaptor arms 1936 and 1938 to the construct. The Type IIs restrictionendonuclease recognition site is shown at 1922, the site of restrictionis shown at 1920, the nick Type IIs restriction endonuclease recognitionsite in the target nucleic acid fragment is shown at 1918 and the nickin the first adaptor is shown at 1934. The process can be repeated toadd as many adaptors as are desired. As shown here, the first addedadaptor had one Type IIs restriction endonuclease recognition site;however, in other aspects, the first added adaptor may have two Type IIsrestriction endonuclease recognition sites to allow for preciseselection of target nucleic acid size for the construct.

In one aspect, adaptors can be designed to have sequence-specificnickase sites surrounding or partially overlapping the Type IIsrestriction endonuclease recognition site. By utilizing the nickase, theType IIs restriction endonuclease recognition site(s) of each adaptorcan be selectively protected from methylation. In further embodiments,the nickase may recognize another sequence or site, but will cut at theType IIs restriction endonuclease recognition site. Nickases areendonucleases recognize a specific recognition sequence indouble-stranded DNA, and cut one strand at a specific location relativeto the recognition sequence, thereby giving rise to single-strandedbreaks in duplex DNA and include but are not limited to Nb.BsrDI,Nb.BsmI, Nt.BbvCI, Nb.Bbv.Nb.BtsI and Nt.BstNBI. By employing acombination of sequence-specific nickase and Type IIs restrictionendonuclease, all Type IIs restriction endonuclease recognition sites inthe target nucleic acid as well as the Type IIs restriction endonucleaserecognition sites in any previously-inserted adaptor can be protectedfrom digestion (assuming, of course, the Type IIs restrictionendonuclease is nick sensitive, i.e., will not bind at a recognitionsite that has been nicked).

FIG. 20 is a schematic representation of an embodiment of methods of theinvention where a desired position of a second adaptor relative to afirst adaptor is selected using methylation and sequence-specificnickases. FIG. 20 shows genomic DNA of interest (target nucleic acid)2002 having a Type IIs restriction endonuclease recognition site at2004. The genomic DNA is fractionated or fragmented in process 2005 toproduce fragments 2006 having a Type IIs restriction endonucleaserecognition site 2004. Adaptor arms 2008 and 2010 are ligated tofragment 2006 in process 2007. Fragment 2006 with adaptor arms 2008 and2010 (a library construct) is circularized in process 2009 and amplifiedby circle dependent amplification in process 2011, resulting in ahighly-branched concatemer of alternating target nucleic acid fragments2006 (with the Type IIs restriction endonuclease recognition site at2004) and first adaptors 2012.

In process 2013, a sequence-specific nickase 2030 is used to nick thenucleic acid in or near specific Type IIs restriction endonucleaserecognition sites in the adaptor in the library construct therebyblocking methylation of these sites. Here, the Type IIs restrictionendonuclease recognition sites in adaptor arms 2012 and 2014 are nickedby sequence-specific nickase 2030. In process 2015, un-nicked Type IIsrestriction endonuclease recognition sites in the construct aremethylated—here, methylation 2016 of the Type IIs restrictionendonuclease recognition site 2004)—protecting these sites from Type IIsrestriction endonuclease recognition. However, the Type IIs restrictionendonuclease recognition sites in adaptors 2012 and 2014 are notmethylated due to the presence of the nicks.

At process 2017, the nicks are repaired in the library construct,resulting in a library construct where the Type IIs restrictionendonuclease recognition site in adaptors 2012 are available forrecognition and restriction 2018, and the Type IIs restrictionendonuclease recognition site in the genomic fragment 2004, is not. Themethylated construct is then ligated to an second pair of adaptor arms,circularized, and amplified via circle dependent amplification atprocess 2021, resulting in a concatemer of alternating target nucleicacid fragments 2006 (with the Type IIs restriction endonucleaserecognition site at 2004), first adaptors 2012 and second adaptors 2020.Next, in process 2023, sequence-specific nicking is performed again,this time with a sequence-specific nickase that recognizes a site in thesecond adaptor 2020 to block methylation of the Type IIs restrictionendonuclease recognition site in the second adaptor 2020, but not theother Type IIs restriction endonuclease recognition sites in theconstruct (i.e., the Type IIs restriction endonuclease recognition site2004 in the fragment and the Type IIs restriction endonucleaserecognition site in first adaptor 2012). The process then continues withmethylation 2015, and further adaptor arms are added, if desired.Different sequence-specific nickase sites are used in each differentadaptor, allowing for sequence-specific nicking throughout the process.

FIG. 21 is a schematic representation of a process where a desiredposition of a second adaptor relative to a first adaptor is selectedusing methylation and sequence-specific methylase blockers. FIG. 21shows genomic DNA of interest (target nucleic acid) 2212 having a TypeIIs restriction endonuclease recognition site at 2214. The genomic DNAis fractionated or fragmented in process 2105 to produce fragment 2106having a Type IIs restriction endonuclease recognition site 2104.Adaptor arms 2108 and 2110 are ligated to fragment 2106 in process 2107.Fragment 2106 with adaptor arms 2108 and 2110 (a library construct) iscircularized in process 2109 and amplified by circle dependentamplification in process 2111, resulting in a highly-branched concatemerof alternating target nucleic acid fragments 2106 (with the Type IIsrestriction endonuclease recognition site at 2104) and first adaptors2112.

In process 2113, a sequence-specific methylase blocker 2130 such as azinc finger is used to block methylation in specific Type IIsrestriction endonuclease recognition sites in the library construct.Here, the Type IIs restriction endonuclease recognition sites in adaptorarms 2112 and 2114 are blocked by methylase blocker 2130. When selectingthe methylase blocker and the Type IIs restriction endonucleases forthis process, it is not necessary that the two entities recognize thesame site sequence or that one entity recognizes a subsequence of theother entity. The blocker sequences may be up- or downstream from theType IIs restriction endonuclease recognition site, but are of aconfiguration that the methylase blocker blocks the site (such as with azinc finger or other nucleic acid binding protein or other entity). Inprocess 2115, unprotected Type IIs restriction endonuclease recognitionsites in the construct are methylated—here, methylation 2116 of the TypeIIs restriction endonuclease recognition site 2104)—protecting thesesites from Type IIs restriction endonuclease recognition. However, theType IIs restriction endonuclease recognition sites in adaptors 2112 and2114 are not methylated due to the presence of the methylase blocker.

At process 2117, the methylase blocker is released from the libraryconstruct, resulting in a library construct where the Type IIsrestriction endonuclease recognition site in adaptors 2112 are availablefor recognition and restriction 2118, and the Type IIs restrictionendonuclease recognition site in the genomic fragment 2104, is not. Themethylated construct is then ligated to an second pair of adaptor arms,circularized, and amplified via circle dependent amplification atprocess 2121, resulting in a concatemer of alternating target nucleicacid fragments 2106 (with the Type IIs restriction endonucleaserecognition site at 2104), first adaptors 2112 and second adaptors 2120.Next, in process 2123, methylase blocking is performed again, this timewith a methylase blocker that recognizes a site in the second adaptor2120 to block methylation of the Type IIs restriction endonucleaserecognition site in the second adaptor 2120, but not the other Type IIsrestriction endonuclease recognition sites in the construct (i.e., theType IIs restriction endonuclease recognition site 2104 in the fragmentand the Type IIs restriction endonuclease recognition site in firstadaptor 2112). The process then continues with methylation 2115, andfurther adaptor arms are added, if desired. Different methylase blockersites are used in each different adaptor, allowing for sequence-specificmethylase blocking throughout the process. Though FIGS. 9 and 21 showinsertion of a second adaptor in relation to a first, it should beunderstood that the process is applicable to adaptors added subsequentlyto the second adaptor, creating library constructs with up to four, six,eight, ten or more inserted adaptors.

FIG. 22 is a schematic illustration of a process where a desiredposition of a second adaptor relative to a first adaptor is selectedusing methylation and uracil degradation. FIG. 22 shows genomic DNA ofinterest 2202 having a Type IIs restriction endonuclease recognitionsite at 2204. The genomic DNA is fractionated or fragmented in process2205 to produce fragments 2206 having a Type IIs restrictionendonuclease recognition site 2204. Adaptor arms 2208 and 2210 areligated to fragment 2206 in process 2207. Fragment 2206 with first andsecond adaptor arms 2208 and 2210 (a library construct) are amplified byPCR in process 2211, using uracil-modified primers 2212 complementary toadaptor arms 2208 and 2210. The primers generate a PCR product withuracils at or close to the Type IIs restriction endonuclease recognitionsite. In process 2213, the uracils are specifically degraded using,e.g., uracil-DNA glycosylase enzyme (Krokan, et al., (1997) Biochem. J.325:1-16), leaving a PCR product that is single-stranded in the Type IIsrestriction endonuclease recognition site region. As shown, uracilincorporation and degradation may be used to render the Type IIsrestriction endonuclease recognition site single-stranded; however, asdescribed further herein, other methods may be employed to render theseregions single-stranded including use of 3′ or 5′ exonucleases in alimited digest.

In process 2215, a sequence-specific methylase is used to methylatebases in each double-stranded Type IIs restriction endonucleaserecognition site (here, there is methylation 2214 of the Type IIsrestriction endonuclease recognition site 2204), to protect these sitesfrom Type IIs restriction endonuclease recognition. However, thesingle-stranded Type IIs restriction endonuclease recognition sites infirst and second adaptor arms 2208 and 2210 are not methylated, and,once circularized and ligated 2217, the Type IIs restrictionendonuclease recognition site re-forms 2216 such that this Type IIsrestriction endonuclease recognition site is available for restriction.When selecting the methylase and the Type IIs restriction endonucleasesfor this process, it is necessary that the two enzymes recognize thesame sequence or that one enzyme recognizes a subsequence (sequencewithin the sequence) of the other enzyme. The circularized construct isthen cut with the Type IIs restriction endonuclease in process 2219where the Type IIs restriction endonuclease recognition site isindicated at 2218 and the construct is cut at 2220, resulting in alinearized construct available for ligation of a second set of adaptorarms to be added to the construct in process 2221.

Ligation process 2221 adds first 2222 and second 2224 adaptor arms ofthe second adaptor to the linearized construct, and a secondamplification is performed by PCR at process 2223, again usinguracil-modified primers 2226 complementary to adaptor arms 2222 and2224. As before, the primers generate a PCR product with uracils closeto the Type IIs restriction endonuclease recognition site. In process2225, the uracils are specifically degraded leaving a PCR product thatis single-stranded in the Type IIs restriction endonuclease recognitionsite region of the first and second adaptor arms 2222 and 2224 of thesecond adaptor. In process 2227, the sequence-specific methylase againis used to methylate bases in the double-stranded Type IIs restrictionendonuclease recognition sites in the target nucleic acid fragment(again, there is methylation 2214 of the Type IIs restrictionendonuclease recognition site 2204) and in the Type IIs restrictionendonuclease recognition site of the first adaptor 2228 protecting thesesites from Type IIs restriction endonuclease recognition. The methylatedconstruct is then circularized at process 2229, where the Type IIsrestriction endonuclease recognition site in the first and second arms2222 and 2224 of the second adaptor is re-formed 2230 and the process isrepeated where the circularized construct is cut again with the Type IIsrestriction endonuclease in process 2219 to generate another linearizedconstruct (this one with first and second adaptors already added)available for ligation of a third pair of adaptor arms to the construct.The process can be repeated to add as many adaptors as are desired. Asshown here, the first added adaptor had one Type IIs restrictionendonuclease recognition site; however, in other aspects, the firstadded adaptor may have two Type IIs restriction endonuclease recognitionsites to allow for precise selection of target nucleic acid size for theconstruct.

In addition to the above methods for controlled insertion of multipleinterspersed adaptors, constructs comprising adaptors in specificorientations may further be selected by enriching a population ofconstructs for those with adaptors in the desired orientations. Suchenrichment methods are described in U.S. Ser. Nos. 60/864,992 filed Nov.9, 2006; 11/943,703, filed Nov. 2, 2007; 11/943,697, filed Nov. 2, 2007;11/943,695, filed Nov. 2, 2007; and PCT/US07/835,540; filed Nov. 2,2007, all of which are incorporated by reference in their entirety forall purposes and in particular for all teachings related to methods andcompositions for selecting for specific orientations of adaptors.

II.E. Making DNBs

Any of the nucleic acid templates of the invention described above canbe used to generate nucleic acid nanoballs, which are also referred toherein as “DNA nanoballs,” “DNBs”, and “amplicons”. These nucleic acidnanoballs are generally concatemers comprising multiple copies of anucleic acid template of the invention, although nucleic acid nanoballsof the invention may be formed from any nucleic acid molecule using themethods described herein. In certain aspects, DNBs comprise repeatingmonomeric units, each monomeric unit comprising one or more adaptors anda target nucleic acid. In further embodiments, populations of DNBs areformed using methods described herein, such that population includesDNBs with different target sequences, such that together the populationof DNBs comprise one or more genome equivalents of one or more entiregenomes.

In one aspect, rolling circle replication (RCR) is used to createconcatemers of the invention. The RCR process has been shown to generatemultiple continuous copies of the M13 genome, (Blanco, et al., (1989) JBiol Chem 264:8935-8940). In such a method, a nucleic acid is replicatedby linear concatemerization. Guidance for selecting conditions andreagents for RCR reactions is available in many references available tothose of ordinary skill, including U.S. Pat. Nos. 5,426,180; 5,854,033;6,143,495; and 5,871,921, each of which is hereby incorporated byreference in its entirety for all purposes and in particular for allteachings related to generating concatemers using RCR or other methods.

Generally, RCR reaction components include single stranded DNA circles,one or more primers that anneal to DNA circles, a DNA polymerase havingstrand displacement activity to extend the 3′ ends of primers annealedto DNA circles, nucleoside triphosphates, and a conventional polymerasereaction buffer. Such components are combined under conditions thatpermit primers to anneal to DNA circle. Extension of these primers bythe DNA polymerase forms concatemers of DNA circle complements. In someembodiments, nucleic acid templates of the invention are double strandedcircles that are denatured to form single stranded circles that can beused in RCR reactions. In some embodiments, amplification of circularnucleic acids may be implemented by successive ligation of shortoligonucleotides, e.g., 6-mers, from a mixture containing all possiblesequences, or if circles are synthetic, a limited mixture of these shortoligonucleotides having selected sequences for circle replication, aprocess known as “circle dependent amplification” (CDA). “Circledependant amplification” or “CDA” refers to multiple displacementamplification of a double-stranded circular template using primersannealing to both strands of the circular template to generate productsrepresenting both strands of the template, resulting in a cascade ofmultiple-hybridization, primer-extension and strand-displacement events.This leads to an exponential increase in the number of primer bindingsites, with a consequent exponential increase in the amount of productgenerated over time. The primers used may be of a random sequence (e.g.,random hexamers) or may have a specific sequence to select foramplification of a desired product. CDA results in a set of concatemericdouble-stranded fragments being formed.

Concatemers may also be generated by ligation of target DNA in thepresence of a bridging template DNA complementary to both beginning andend of the target molecule. A population of different target DNA may beconverted in concatemers by a mixture of corresponding bridgingtemplates.

In some embodiments, a subset of a population of nucleic acid templatesmay be isolated based on a particular feature, such as a desired numberor type of adaptor. This population can be isolated or otherwiseprocessed (e.g., size selected) using conventional techniques, e.g., aconventional spin column, or the like, to form a population from which apopulation of concatemers can be created using techniques such as RCR.

Methods for forming DNBs of the invention are described in PublishedPatent Application Nos. WO2007120208, WO2006073504, WO2007133831, andUS2007099208, and U.S. Patent Application Nos. 60/992,485; 61/026,337;61/035,914; 61/061,134; 61/116,193; 61/102,586; Ser. Nos. 12/265,593;12/266,385; 11/938,096; 11/981,804; Nos. 11/981,797; 11/981,793;11/981,767; 11/981,761; 11/981,730, filed Oct. 31, 2007; 11/981,685;11/981,661; 11/981,607; 11/981,605; 11/927,388; 11/927,356; 11/679,124;11/541,225; 10/547,214; 11/451,692; and 11/451,691, all of which areincorporated herein by reference in their entirety for all purposes andin particular for all teachings related to forming DNBs.

III. Methods of Obtaining Sequence Information

Nucleic acids, nucleic acid fragments, and template nucleic acidconstructs isolated and generated in accordance with any of the methodsdescribed herein can be used in applications for obtaining sequenceinformation. Such methods include sequencing and detecting specificsequences in target nucleic acids (e.g., detecting particular targetsequences (e.g. specific genes) and/or identifying and/or detectingSNPs). The methods described herein can also be used to detect nucleicacid rearrangements and copy number variation. Nucleic acidquantification, such as digital gene expression (i.e., analysis of anentire transcriptome—all mRNA present in a sample) and detection of thenumber of specific sequences or groups of sequences in a sample, canalso be accomplished using the methods described herein.

In one aspect, the fragments and nucleic acid constructs generated inaccordance with the present invention provide the advantage of allowingshort sequence reads to be combined and assembled to provide sequenceinformation on longer contiguous regions of the target nucleic acid(contiguous segments of nucleic acids comprising two or more nucleotidesin a row are also referred to herein as “contigs”). As used herein,“sequence reads” refers to identifying or determining the identity ofone or more nucleotides in a region of a target nucleic acid. Generallysequence reads provide information on the sequence of a segment of anucleic acid comprising two or more contiguous nucleotides. In certainaspects, unchained base reads are used to generate sequence information,as described in Drmanac et al., (2010), Science, 327: 78-81 andsupplementary online material, which is hereby incorporated by referencein its entirety and in particular for all teachings related to methodsand compositions for sequencing nucleic acids.

III.A. LFR

In one aspect, Long Fragment Read (LFR) sequencing methods are used withany of the fragments or nucleic acid template constructs or DNAnanoballs described herein. Although the following is describedprimarily in terms of genomic nucleic acid fragments, it will beappreciated that any nucleic acid molecules would be amenable to be themethods described below. General LFR methods are described in U.S.patent application Ser. No. 11/451,692, filed Jun. 13, 2006, now U.S.Pat. No. 7,709,197, and in U.S. patent application Ser. No. 12/329,365,filed Dec. 5, 2008, each of which is hereby incorporated by reference inits entirety and in particular for all teachings related to LFR andsequencing using LFR methods.

In general, LFR methods include physical separation of long genomic DNAfragments across many different aliquots such that the probability ofany given region of the genome of both the maternal and paternalcomponent in the same aliquot is very rare. By placing a uniqueidentifier in each aliquot and analyzing many aliquot in the aggregate,long fragments of DNA can be assembled into a diploid genome, e.g. thesequence of each parental chromosome can be obtained.

Aliquots of LFR fragments are also referred to herein as “LFR libraries”and “LFR aliquot libraries”. These LFR libraries may include tagged andnon-tagged fragments.

LFR provides a novel and inexpensive way of DNA preparation and taggingwith related algorithms and software to enable an accurate assembly ofseparate sequences of parental chromosomes (i.e., complete haplotyping)in diploid genomes (such as in human embryonic or adult somatic cells)at significantly reduced experimental and computational costs (below$1000). This process, universally applicable with any existing genome ormetagenome sequencing technology including future longer read (˜1 kb)methods, is in many ways equivalent to sequencing single DNA moleculesof greater than 100 kb in length, a technically challenging proposition.The proposed long fragment read (LFR) process does not requireexpensive, less accurate and lower yield single molecule detection. TheLFR process is based upon the stochastic physical separation of a genomein long fragments (100-1000 kb) into many aliquots in such a way thateach aliquot contains 10% or less of a haploid genome.

LFR methods as described herein find particular use when the startingamount of DNA to be analyzed is low. In some embodiments, LFR methods ofthe invention are used to analyze the genome of an individual cell. Infurther embodiments, LFR methods of the invention are used to analyzethe genomes from 1-100 cells. In still further embodiments, LFR methodsof the invention are used to analyze the genomes from 1-5, 5-10, 2-90,3-80, 4-70, 5-60, 6-50, 7-40, 8-30, 9-20, and 10-15 cells. The processfor isolating DNA when small numbers of cells are used is similar to themethods described above, but occurs in a smaller volume. As will beappreciated, LFR methods of the present invention can also be used whenthe starting amount of DNA is high (i.e., greater than the equivalentfrom 50-100 cells).

In some embodiments after the DNA is isolated and before it is dividedinto separate aliquots (such as into individual wells of a multiwellplate or into different emulsion droplets, as described in furtherdetail below), the genomic DNA is carefully fragmented to avoid loss ofmaterial, particularly to avoid loss of sequence from the ends of eachfragment, since loss of such material will result in gaps in the finalgenome assembly. In some cases, sequence loss is avoided through use ofan infrequent nicking enzyme, which creates starting sites for apolymerase, such as φ29 polymerase, at distances of approximately 100 kbfrom each other. As the polymerase creates the new DNA strand, itdisplaces the old strand, with the end result being that there areoverlapping sequences near the sites of polymerase initiation, resultingin very few deletions of sequence.

In specific embodiments, fragments produced according to one or moreembodiments of CoRE as described above are used in the LFR methodsdescribed herein. In general, the process of isolating DNA from a samplewill result in 100 kb fragments. These fragments may then be furtherfragmented or used to generate shorter fragments using the methodsdescribed herein (including CoRE) either before or after or both beforeand after being divided into separate aliquots.

In some embodiments, DNA is isolated from a sample and then aliquotedinto a number of different separate mixtures (such separate mixtures arealso referred to interchangeably herein as “aliquots”). Afteraliquoting, the DNA in the separate mixtures is then fragmented, usingany of the methods described herein, including any of the embodiments ofCoRE fragmentation discussed above. The DNA in the separate mixtures mayalso be used to generate shorter fragments by using a controlled DNAsynthesis or amplification using the DNA in the separate mixtures astemplates. Such synthesis and amplification methods are known in the artand in general use multiple spaced-apart primers corresponding todifferent regions of the DNA in the separate mixtures to replicateand/or amplify the DNA. In such embodiments, a second population of DNAfragments is formed that are of shorter length than the longer fragmentsfrom which they are derived. In further embodiments, the DNA in theseparate mixtures is fragmented (or used as a template to produceshorter fragments) multiple times. In still further embodiments, afterone or more rounds of fragmenting, the DNA in each aliquot is taggedwith adaptor tags in accordance with the methods described herein.

In one embodiment, genomic fragments (either before or afterfragmentation) are aliquoted such that the nucleic acids are diluted toa concentration of approximately 10% of a haploid genome per aliquot. Atsuch a level of dilution, approximately 95% of the base pairs in aparticular aliquot are non-overlapping. This method of aliquoting, alsoreferred to herein as a long fragment read (LFR) fragmentation method,can in particular embodiments be used on large molecular weightfragments isolated according to the methods described above and furtherherein. LFR usually begins with a short treatment of genomic nucleicacids, usually genomic DNA, with a 5′ exonuclease to create 3′single-stranded overhangs. Such single stranded overhangs serve asmultiple displacement amplification (MDA) initiation sites. The 5′exonuclease treated DNA is then diluted to sub-genome concentrations anddispersed across a number of aliquots. In some embodiments, thesealiquots are dispersed across a number of wells in a multiwell plate. Inother embodiments, the aliquots are contained in different emulsiondroplets, as described in further detail below. The fragments in eachaliquot are amplified, usually using an MDA method that includes one ormore of the additives described above for reducing or preventing bias.

As discussed above, to achieve an appropriate separation of fragments,in general the DNA is aliquoted/diluted to a concentration ofapproximately 1-15% of a haploid genome per aliquot. In furtherembodiments, the DNA is aliquoted to a concentration of approximately10% of a haploid genome per aliquot. At this concentration, 95% of thebase pairs in an aliquot are non-overlapping. Dilution to sub-genomealiquots results in a statistical separation such that maternal andpaternal fragments will usually land in different aliquots. It should beappreciated that the dilution factor can depend on the original size ofthe fragments. Techniques that allow larger fragments result in a needfor fewer aliquots, and those that result in shorter fragments mayrequire a larger number of aliquots.

In further embodiments, the DNA is diluted (i.e., aliquoted) to aconcentration of approximately 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, and 15% of a haploid genome per aliquot. In still furtherembodiments, the DNA is diluted to a concentration of less than 1% of ahaploid genome per aliquot. In yet further embodiments, the DNA isdiluted to about 0.1-1%, 0.2-0.9%, 0.3-0.8%, 0.4-0.7%, and 0.5-0.6% of ahaploid genome per aliquot.

In some embodiments, the fragments are amplified before, after or bothbefore and after aliquoting. In further embodiments, the fragments ineach aliquot are further fragmented and then tagged with an adaptor tagsuch that fragments from the same aliquot will all comprise the same tagadaptor; see for example US 2007/0072208, hereby incorporated byreference in its entirety, and in particular for the discussions ofadditional aliquoting and coverage. In certain embodiments, fragmentsare not amplified after aliquoting, but are further fragmented using anyof the methods discussed herein and known in the art. In certainembodiments, DNA is not amplified prior to aliquoting, but is bothfragmented and amplified after aliquoting. DNA in separate aliquots mayalso in further embodiments be fragmented and amplified multiple times.

In still further embodiments, multiple tiers of aliquoting are used inLFR methods of the invention. Aliquots in one or more tiers may betagged such that aliquots in each subsequent tier can be identified bytheir aliquot of origin in the previous tier. The fragments in eachround of aliquot may or may not be amplified and/or further fragmentedprior to the next round of aliquoting.

In further embodiments, sequence information obtained from LFR aliquotsare assembled using bioinformatics techniques that fully utilizeinformation from a large number of ˜10 Mb aliquots, which reduces thecomputation effort (i.e., capital cost of computers) by about 100 fold.The added cost of reading 10-base tags (10% in sequencing reagents andinstrument time for 2×50-base mate-pair reads) is offset multiple timesby this savings in computation and increased sequence accuracy.

In a further embodiment, methods of the present invention are integratedwith high throughput low cost short read DNA sequencing technology, suchas those described in published patent application numbers WO2007120208,WO2006073504, WO2007133831, and US2007099208, and U.S. patentapplication Ser. Nos. 11/679,124; 11/981,761; 11/981,661; 11/981,605;11/981,793; 11/981,804; 11/451,691; 11/981,607; 11/981,767; 11/982,467;11/451,692; 11/541,225; 11/927,356; 11/927,388; 11/938,096; 11/938,106;10/547,214; 11/981,730; 11/981,685; 11/981,797; 11/934,695; 11/934,697;11/934,703; 12/265,593; 11/938,213; 11/938,221; 12/325,922; 12/252,280;12/266,385; 12/329,365; 12/335,168; 12/335,188; and 12/361,507 all ofwhich are incorporated herein by reference in their entirety for allpurposes and in particular for all teachings related to DNA sequencing.

III.A.1. Tagging

Fragments in different aliquots can be tagged with one or more adaptortags in order to identify fragments that were contained in the samealiquot. In some embodiments, fragments in different aliquots can betagged with one or more “adaptor tags” (sometimes referred to as“tagging sequences”, “tags” or “barcodes” (note these were also referredto as “adaptors” in U.S. Provisional App. No. 61/187,162, filed Jun. 15,2009). Adaptor tags are in general oligonucleotides that are ligated tonucleic acid fragments to serve as an identifier during LFR methodsdescribed herein. Although adaptor tags are in general sequenced alongwith the target fragments to which they are attached, adaptor tags donot generally (but in some embodiments can) serve the same functions asadaptors as described herein for constructing nucleic acid constructs orin cPAL sequencing methods. In general, the sequence of an adaptor tagis used to identify the aliquot of origin of the fragment to which thattag is attached.

As outlined above, some embodiments of LFR do not require adaptor tags;in these embodiments, the LFR aliquots are put in different vessels,such as the microtiter plate embodiments discussed herein. In theseembodiments, the LFR fragments can again be additionally fragmented,without the addition of adaptor tags, as long as the source of eachaliquot is traced.

Alternatively, as described in detail below, the aliquots are taggedwith adaptor tags to identify fragments that were contained in the samealiquot. Adaptor tags can be added in a variety of ways, as outlinedbelow. In some cases, adaptor tags can be added (as for other adaptoradditions described herein) in such a manner as to prevent“polymerization” of the adaptor tags.

In embodiments that utilize tagging, fragments in each aliquot aretagged with one or more adaptor tags. In some embodiments, the adaptortag is designed in two segments—one segment is common to all wells andblunt end ligates directly to the fragments using methods describedfurther herein. The second segment is unique to each well and may alsocontain a “barcode” sequence such that when the contents of each wellare combined, the fragments from each well can be identified. FIG. 27illustrates some exemplary barcode adaptor tags that can be added to thefragments for this aspect of the invention.

In many aspects of the present invention, it is useful to have fragmentsthat are repaired to have blunt ends, and in some cases, it can bedesirable to alter the chemistry of the termini such that the correctorientation of phosphate and hydroxyl groups is not present, thuspreventing “polymerization” of the target sequences. The control overthe chemistry of the termini can be provided using methods known in theart and described in further detail above in relation to furthertreatment of fragments and in relation to ligation of adaptors to targetnucleic acids. Such methods are also applicable to controlling thedirectionality of ligating adaptor tags to fragments in the methodsdescribed herein. Further methods for controlling the orientation ofadaptor tag orientation are illustrated in FIG. 7, in which the primersand uracil positions are chosen such that either the “upstream” or“downstream” recognition site may be selectively protected frominactivation or inactivated. For example, in FIG. 7, the two differentadaptor tag arms (represented as rectangles) each comprise a recognitionsite for a restriction endonuclease (represented by the circle in oneadaptor tag arm and by a triangle in the other). If the adaptor tag armwith the recognition site represented by the circle needs to beprotected using the above-described uracil degradation method, then theuracil-modified amplification primers are designed to incorporateuracils into that recognition site. Then upon uracil degradation, thatadaptor tag arm is rendered single stranded (represented by thehalf-rectangles), thus protecting that recognition site frominactivation.

In some circumstances, the use of phosphatase eliminates all thephosphate groups, such that all ends contain hydroxyl groups. Each endcan then be selectively altered to allow ligation between the desiredcomponents. One end of the fragments can then be “activated”, in someembodiments by treatment with alkaline phosphatase.

FIG. 27 provides a schematic illustration of some embodiments of adaptortag design for use as a tag in accordance with the LFR methods describedherein. Generally, the adaptor tag is designed in two segments—onesegment is common to all aliquots and blunt end ligates directly to thefragments using methods described further herein. The “common adaptortag” can be used as a control for any potential concentrationdifferences between aliquots. In the embodiment pictured in FIG. 27, the“common” adaptor tag is added as two adaptor tag arms—one arm is bluntend ligated to the 5′ end of the fragment and the other arm is blunt endligated to the 3′ end of the fragment. The second segment of the adaptortag is a “barcode” segment that is unique to each well. This barcode isgenerally a unique sequence of nucleotides, and each fragment in aparticular well is given the same barcode. Thus, when the taggedfragments from all the aliquots are re-combined for sequencingapplications, fragments from the same aliquot can be identified throughidentification of the barcode adaptor tag. In the embodiment illustratedin FIG. 27, the barcode is ligated to the 5′ end of the common adaptortag arm. The common adaptor tag and the barcode adaptor tag can beligated to the fragment sequentially or simultaneously. As is describedin further detail herein, the ends of the common adaptor tag and thebarcode adaptor tag can be modified such that each adaptor tag segmentwill ligate in the correct orientation and to the proper molecule. Suchmodifications prevent “polymerization” of the adaptor tag segments or ofthe fragments by ensuring that the fragments are unable to ligate toeach other and that the adaptor tag segments are only able to ligate tothe fragment in the desired orientation. Such modifications are alsodiscussed in detail in the sections above regarding controlling adaptorligation to target nucleic acids for producing nucleic acid templateconstructs of the invention.

In further embodiments, a three segment design is utilized for theadaptor tags used to tag fragments in each well. This embodiment issimilar to the barcode adaptor tag design described above, except thatthe barcode adaptor tag segment is itself split into two segments (seeFIG. 27). This design allows for a wider range of possible barcodes byallowing combinatorial barcode adaptor tag segments to be generated byligating different barcode segments together to form the full barcodesegment. This combinatorial design provides a larger repertoire ofpossible barcode adaptor tags while reducing the number of full sizebarcode adaptor tags that need to be generated.

In one embodiment, construction of an LFR library of multiple aliquotsof tagged fragments involves using different adaptor tag sets. A and Badaptor tags are easily modified to each contain a differenthalf-barcode sequence to yield thousands of combinations. In certainembodiments, the half-barcode sequences are incorporated into the sameadaptor tag. This can be achieved by breaking the B adaptor tag into twoparts, each with a half barcode sequence separated by a commonoverlapping sequence used for ligation (FIG. 28E). The two tagcomponents have 4-6 bases each. An 8-base (2×4 bases) tag set is capableof uniquely tagging 65,000 aliquots. One extra base (2×5 bases) willallow error detection and 12 base tags (2×6 bases, 12 million uniquebarcode sequences) can be designed to allow substantial error detectionand correction in 10,000 or more aliquots using Reed-Solomon design.Methods for designing adaptor tags are further disclosed in U.S. patentapplication Ser. No. 12/697,995, filed Feb. 1, 2010, which is herebyincorporated by reference in its entirety for all purposes and inparticular for all teachings related to Reed-Solomon algorithms andtheir use in designing adaptor tags (which are also referred to as“adaptors” in that application).

In still further embodiments, the ligation of the adaptor tag iscontrolled for orientation, that is, the present invention provides fordirectional ligation of the adaptor tag. Such directional ligation mayutilize any of the methods described herein for ligating adaptors totarget nucleic acids. In an exemplary embodiment, half-adaptor tags(also referred to herein as tag components and adaptor tag segments) areligated on each side of DNA fragments in two separate steps. The firsthalf-adaptor tag is blocked on its 3′ end by incorporation of a dideoxynucleotide on one strand, thus allowing ligation only to the 3′ ends ofDNA fragments. Thus, a double-stranded fragment has a half-adaptor tagligated to the 3′ terminus of each strand of the fragment (i.e., thereis a half-adaptor tag ligated to the 3′ end of the “Watson” strand andto the “Crick” strand). These “half-tagged” fragments are then denaturedand combined with primers complementary to the ligated adaptor tag andpolymerase to produce double-stranded DNA from each DNA fragment strandligated to a first half adaptor tag. In certain embodiments, the firsthalf-adaptor tag comprises a barcode or half-barcode as discussed infurther detail herein. The second half-adaptor tag (which in someembodiments does not contain a barcode) can then be ligated to the newlycreated 3′ end of the replicated fragment comprising the firsthalf-adaptor tag. An advantage of this sequential method of adding eachhalf-adaptor tag to the fragments is that only those fragments ligatedto the first half-adaptor tag will then undergo ligation with the secondhalf-adaptor tag. As will be appreciated, multiple “half-adaptor tags”can be added during each cycle—in other words, 1 or more tag componentscan be directionally ligated to a chosen terminus of each fragment, andthen upon denaturation and replication, 1 or more additional tagcomponents can be added to the newly created 3′ ends. Thus, differentsets of tag components can be used in a variety of combinations toproduce combinatorial tags for tagging fragments.

In still further embodiments, the first half-adaptor tag is blocked onthe 5′ end, allowing ligation only to the 5′ end of the DNA fragments,and the second half-adaptor tag is blocked on the 3′ end, allowingligation only to the 3′ end of the DNA fragments. Thus, both halves ofthe adaptor tag can be ligated to the fragments simultaneously in thisembodiment.

In further embodiments, methods of adding adaptor tags or other tags tofragments are conducted in accordance with the disclosure of addingadaptors in WO2007120208, WO2006073504, WO2007133831, and US2007099208,and U.S. patent application Ser. Nos. 11/679,124; 11/981,761;11/981,661; 11/981,605; 11/981,793; 11/981,804; 11/451,691; 11/981,607;11/981,767; 11/982,467; 11/451,692; 11/541,225; 11/927,356; 11/927,388;11/938,096; 11/938,106; 10/547,214; 11/981,730; 11/981,685; 11/981,797;11/934,695; 11/934,697; 11/934,703; 12/265,593; 11/938,213; 11/938,221;12/325,922; 12/252,280; 12/266,385; 12/329,365; 12/335,168; 12/335,188;and 12/361,507, each of which is hereby incorporated by reference in itsentirety for all purposes and in particular for all teachings related toadaptors.

After the fragments in each well are tagged, all of the aliquots can insome embodiments be combined to form a single population. Sequenceinformation obtained from these tagged fragments will be identifiable asbelonging to a particular aliquot by the barcode tag adaptor tagsattached to each fragment.

III.A.2. Multi-Well Format LFR

In many embodiments, each aliquot is contained in a separate well of amulti-well plate (for example, a 384 or 1536 well microtiter plate). Itwill be appreciated that although the following discussion of LFR isprovided in terms of a multi-well plate, that any number of differenttypes of containers and systems can be used to hold the differentaliquots generated in this method. Such containers and systems are wellknown in the art and it would be apparent to one of skill in the artwhat types of containers and systems would be appropriate to use inaccordance with this aspect of the invention.

In some embodiments, a 10% genome equivalent is aliquoted into each wellof a multiwell plate. If a 384 well plate is used, a 10% genomeequivalent aliquot into each well results in each plate comprising 38genomes in total. In further embodiments, a 5-50% genome equivalent isaliquoted into each well. As noted above, the number of aliquots andgenome equivalents used in LFR methods of the present invention candepend on the original fragment size.

After separation across multiple wells, the fragments in each well canbe amplified, usually using an MDA method. In certain embodiments, theMDA reaction is a modified 1)₂₉ polymerase-based amplification reaction.Although much of the discussion herein is in terms of an MDA reaction,it will be appreciated by those of skill in the art that many differentkinds of amplification reactions can be used in accordance with thepresent invention, and that such amplification reactions are well knownin the art and described generally in Maniatis et al., MolecularCloning: A Laboratory Manual, 2d Edition, 1989, and Short Protocols inMolecular Biology, ed. Ausubel, et al, hereby incorporated by reference.In certain embodiments, MDA methods used before or after each step ofaliquoting can include additives to reduce amplification bias, as isdiscussed in further detail above.

After amplification of the fragments in each well, the amplificationproducts may be subjected to another round of fragmentation. In someembodiments the above-described CoRE method is used to further fragmentthe fragments in each well following amplification. As discussed above,in order to use the CoRE method, the MDA reaction used to amplify thefragments in each well is designed to incorporate uracils or othernucleotide analogs into the MDA products.

III.A.3. Emulsion Droplets

In certain LFR applications, emulsion droplets are used in thealiquoting and tagging methods. Methods for producing emulsion dropletscontaining nucleic acids and/or reagents for enzymatic reactions areknown in the art—see for example, Weizmann et al., (2006), NatureMethods, Vol. 3 No. 7, pages 545-550, which is hereby incorporated byreference in its entirety for all purposes and in particular for allteachings related to forming emulsions and conducting enzymaticreactions within emulsion droplets.

In some embodiments, nucleic acids isolated from a sample or nucleicacid fragments, including fragments generated using CoRE fragmentationmethods described herein, are contained within emulsion droplets. Insuch embodiments, each droplet generally contains a small number offragments. In LFR methods used for whole genome sequencing, thepopulation of emulsion droplets together will contain fragmentsrepresenting one or more genome equivalents. In further embodiments, thepopulation of emulsion droplets together will contain fragmentsrepresenting 5-15 genome equivalents. In still further embodiments, thepopulation of emulsion droplets together will contain fragmentsrepresenting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19 or 20 genome equivalents.

In further embodiments, two or more adaptor tag components are alsocontained in emulsion droplets. For clarity's sake, emulsion dropletscontaining target nucleic acid fragments are referred to as “targetnucleic acid droplets”, and emulsion droplets containing adaptor tagsare referred to as “adaptor tag droplets”.

In certain embodiments, enzymes such as ligase and other reagents suchas buffers and cofactors are also contained within the target nucleicacid droplets and/or in the adaptor tag droplets. “Chaining” of thefragments or the adaptor tags within the same droplet can be preventedby altering the termini as described in further detail above, such thatligation only occurs between fragments and adaptors in the preferredorientation. Ligase and other reagents may also be included in aseparate set of emulsion droplets.

In still further embodiments, individual target nucleic acid dropletsare combined with individual adaptor tag droplets, such that thedroplets merge. In embodiments in which either the target nucleic aciddroplets or the adaptor tag droplets contain ligase and/or otherreagents for ligation reactions, upon merging of the adaptor tag andnucleic acid droplets, the nucleic acid fragments will ligate to one ormore adaptor tags. In embodiments in which ligase and other reagents areincluded in a separate set of emulsion droplets, ligation will occurupon merging of the individual target nucleic acid droplets, theindividual adaptor tag droplets and the ligase/reagent droplets.

In embodiments in which the adaptor tag droplets contain two or more“half-adaptors” (also referred to herein as “tag components”), mergingof the droplets results in the target nucleic acid fragments in eachdroplet being ligated to unique combinatorial adaptor tags, (FIG.28A-B). Two sets of 100 half barcodes is sufficient to uniquely identify10,000 aliquots (FIG. 2E). However, increasing the number of halfbarcode adapters to over 300 can allow for a random addition of barcodedroplets to be combined with the sample DNA with a low likelihood of anytwo aliquots containing the same combination of barcodes. An advantageof this is that tens of thousands of distinct combinatorial barcodeadaptor tag droplets can be made in large quantities and stored in asingle tube to be used as a reagent for thousands of different LFRlibraries.

In some embodiments, 10,000 to 100,000 or more aliquot libraries (i.e.,emulsion droplets) are used in methods of the invention. In furtherembodiments, the emulsion LFR methods are scaled up by increasing thenumber of initial half barcode adaptor tags. These combinatorial adaptortag droplets are then fused one-to-one with droplets containing ligationready DNA representing less than 1% of the haploid genome (FIG. 28D).Using a conservative estimate of 1 nl per droplet and 10,000 drops thisrepresents a total volume of 10 μl for an entire LFR library; a volumereduction and thus a cost reduction of approximately 400 fold can bepossible. In such embodiments, the emulsion droplets provide the abilityto miniaturize LFR aliquots from microliters to nanoliters and increasethe number of aliquots generally used in such methods from hundreds tothousands (reducing DNA per aliquot from 10% to less than 1%). Such asystem with 10,000 or more emulsion droplets opens the possibility toconduct complete genome sequencing starting with just one cell.

In further embodiments, 1,000 to 500,000 droplets of fragments andadaptor tags are used in methods of the invention. In still furtherembodiments, 10,000-400,000; 20,000-300,000; 30,000-200,000;40-000-150,000; 50,000-100,000; 60,000-75,000 droplets of fragments andadaptor tags are used in methods of the invention. In yet furtherembodiments, at least 1,000, at least 10,000, at least 30,000, and atleast 100,000 droplets of fragments and adaptor tags are used in methodsof the invention.

In further embodiments in which droplets of adaptor tags contain atleast 2, 3, 4, 5, 6, 7, 8, 9, 10 different sets or components of adaptortags, combining these adaptor tag droplets with droplets of nucleic acidfragments results in at least a portion of the resultant combineddroplets having fragments that are tagged with different combinations oftag components. In yet further embodiments, at least 1,000, at least10,000, at least 30,000, and at least 100,000 different droplets containfragments tagged with different combinations of tag components. In stillfurther embodiments, 1,000 to 500,000 droplets contain fragments taggedwith different combinations of tag components. In still furtherembodiments, 10,000-400,000; 20,000-300,000; 30,000-200,000;40-000-150,000; 50,000-100,000; 60,000-75,000 droplets contain fragmentstagged with different combinations of tag components.

In some embodiments, nucleic acids from a sample or nucleic acidfragments generated using any of the methods described herein arecontained within emulsion droplets, as discussed above. Prior tocombining with adaptor tag droplets and tagging, the nucleic acids orfragments within each nucleic acid droplet are fragmented using any ofthe methods described herein. Such fragmentation and then subsequenttagging allows identification of fragments that are contained in thesame droplet and that may also be contiguous segments of the same regionof the genome. Thus, sequence information of the tagged target nucleicacid fragments can be assembled and ordered using the identification ofthe attached tags. In certain embodiments, sequencing of the fragmentsincludes obtaining information about their attached adaptor tags.

In certain embodiments, the size of emulsion droplets is controlledusing methods known in the art in order to prevent shearing and thusfurther fragmentation of the target nucleic acid fragments as they arecontained within the droplets. In some embodiments, 1 nL droplets (thatis, droplets of 100 μm³ volume) are used. It has been shown that 50 kblambda dsDNA forms 1 μm³ balls, and thus 200 kb human genomic dsDNAwould be expected to form ˜2 μm³ cubed balls, which would easily becontained in a 1 nl droplet with minimal shearing due to the containment(emulsion) process. Single stranded DNA, which is the starting step forMDA and is the material generally used to form droplets of the inventionin embodiments in which DNA is amplified prior to or after aliquoting,are even more compact or flexible because it has about a tenth of thepersistence length of dsDNA. In addition, and as discussed in furtherdetail above, adding elements such as spermidine to DNA during thepipetting processes also helps protect DNA from shearing, which is(without being bound by theory) is likely due to the ability ofsubstances such as spermidine to compact DNA.

There are currently several types of microfluidics (e.g., AdvancedLiquid Logic) or pico/nano-droplet (e.g., RainDance Technologies)devices that could be modified to accept LFR reagents and processes.These instruments have pico/nano-drop making, fusing (3000/second) andcollecting functions that are currently fully operational. Such smallvolumes may also help prevent bias introduced by amplification methodsand may also reduce background amplification.

An advantage of using emulsion droplets is that reduction of reactionvolumes to microliter, nanoliter and picoliter levels provides areduction in the costs and time associated with producing LFR libraries.

III.A.4. Advantages and Exemplary Applications of LFR

In one aspect, fragments from LFR aliquot libraries are used to generateDNBs in accordance with the methods described above. These DNBs may thenbe used in sequencing methods known in the art and described in furtherdetail herein.

In a further aspect, initial long DNA fragments are aliquoted and thenfragmented and tagged in each aliquot. These tagged fragments are thenpooled together and at least a portion of the fragments are subsequentlysequenced without amplification. In certain embodiments, about 30%-80%of the fragments are sequenced. In further embodiments, about 35%-70%,40%-65%, 45%-60%, and 50%-55% of the fragments are sequenced. In a stillfurther embodiment, at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% ofthe aliquoted and tagged fragments are sequenced without amplification.

In other embodiments, the fragments are amplified, and then about35%-70%, 40%-65%, 45%-60%, and 50%-55% of the amplified fragments aresequenced. In a further embodiment, at least 30%, 40%, 50%, 60%, 70%,80%, 90%, 95% of the aliquoted and tagged fragments are sequenced afteramplification.

In one aspect, sequence reads from LFR fragments are assembled toprovide sequence information for a contiguous region of the originaltarget nucleic acid that is longer than the individual sequence reads.Sequence reads can be on the order of 20-200 bases or in some methods200-2,000 bases or longer. As discussed in further detail herein,aliquoted fragments are generally about 20-200 kb or even longer than 1Mb. In a further aspect, this assembly relies on the identity of thetags for each fragment to identify fragments that were contained in thesame aliquot. In still further aspects, the tags are oligonucleotideadaptor tags and individual tags are identified by determining at leastpart of the tag sequence. The identities of the tags serve to identifythe aliquot of origin of the attached fragments and can also be used toorder the sequence reads from individual fragments and to differentiatebetween haplotypes. For example, as discussed above, the process ofaliquoting the long fragments in LFR generally results in separatingcorresponding parental DNA fragments into separate aliquots, such thatwith an increasing number of aliquots, the number of aliquots with bothmaternal and paternal haplotypes becomes negligibly small. Thus,sequence reads from fragments in the same aliquot can be assembled andordered. The longer fragments used in this method also help bridge oversegments lacking heterozygous loci or resolve long segmentalduplications.

A further advantage LFR is that sequence information obtained from thelonger fragments can be used to assemble sequences for genomic regionsthat contain repetitive sequences whose length is greater than theindividual sequence reads obtained from whatever sequencing methodologyis used. Such advantages and applications of LFR are also discussed inU.S. patent application Ser. No. 11/451,692, filed Jun. 13, 2006, nowU.S. Pat. No. 7,709,197, and in U.S. patent application Ser. No.12/329,365, filed Dec. 5, 2008, each of which is hereby incorporated byreference in its entirety and in particular for all teachings related toLFR and sequencing using LFR methods.

It is recognized that the advancement of biosciences (including foragriculture and bio-fuel production) and medicine is criticallydependant on accurate low cost and high throughput genome andtranscriptome sequencing. To achieve these benefits the cost ofaccurately sequencing an individual's genome should be very low, such asless than $1000. This cost should include all components of the processsuch as DNA preparation, reagents, sequencing instrument depreciation,and computing.

The present LFR invention can also be used for a fast full de novoassembly without reference sequence (e.g., metagenomics). First, partialassembles can be achieved within each aliquot. A limited alignment ofassembled contigs is then used to find aliquots with overlappingfragments to do full assembly of a shared DNA segment. The assembly ofsegments is then propagated in both directions. A large number of LFRaliquots with less than 0.1% of the genome ensures uniqueness of shorteroverlaps of short reads in de novo assembly (i.e. 12 bases is sufficientfor unique read overlapping in 0.1% of the genome verses the 17 basesrequired for the complete genome) leading to longer sequence contigs atlower read coverage. Read coverage generally refers to the fraction orfold-coverage of a genome.

In one aspect, the present invention encompasses software and algorithmsthat executes protocols in accordance with the above exemplary methodwith high efficiency.

In a further aspect, methods and compositions of the present inventionare used for genomic methylation analysis. There are several methodscurrently available for global genomic methylation analysis. The mosteconomically accessible method involves bisulfate treatment of genomicDNA and sequencing of repetitive elements or a fraction of the genomeobtained by methylation specific restriction enzyme fragmenting. Thistechnique yields information on total methylation, but provides no locusspecific data. The next higher level of resolution uses DNA arrays andis limited by the number of features on the chip. Finally, the highestresolution and the most expensive approach requires bisulfate treatmentand then sequencing of the entire genome. Using LFR techniques of thepresent invention, it is possible to sequence all bases of the genomeand assemble a complete diploid genome with digital information onlevels of methylation for every cytosine position in the human genome(i.e., 5 base sequencing). Further, LFR allow blocks of methylatedsequence of 100 kb or greater to be linked to sequence haplotypes,providing methylation haplotyping, information that is impossible toachieve with any currently available method.

In one non-limiting exemplary embodiment, methylation status is obtainedin a method in which genomic DNA is first aliquoted and denatured forMDA. Next the DNA is treated with bisulfite (a step that requiresdenatured DNA). The remaining preparation follows those methodsdescribed for example in U.S. application Ser. Nos. 11/451,692, filed onJun. 13, 2006 and 12/335,168, filed on Dec. 15, 2008, each of which ishereby incorporated by reference in its entirety for all purposes and inparticular for all teachings related to nucleic acid analysis ofmixtures of fragments according to long fragment read techniques.

In one aspect, MDA will amplify each strand of a specific fragmentindependently yielding for any given cytosine position 50% of the readsas unaffected by bisulfite (i.e., the base opposite of cytosine, aguanine is unaffected by bisulfate) and 50% providing methylationstatus. Reduced DNA complexity per aliquot helps with accurate mappingand assembly of the less informative, mostly 3-base (A, T, G) reads.

Bisulfite treatment has historically been found to fragment DNA.However, careful titration of denaturation and bisulfate buffers canavoid excessive fragmenting of genomic DNA. A 50% conversion of cytosineto uracil can be tolerated in LFR allowing a reduction in exposure ofthe DNA to bisulfite to minimize fragmenting. In some embodiments, somedegree of fragmenting after aliquoting is acceptable as it would notaffect haplotyping.

In one aspect, methods of the present invention produce quality genomicdata from single cells. The ability to sequence single cells will openup many new avenues in genome research and diagnostics. Assuming no lossof DNA, there is a benefit to starting with a low number of cells (10 orless) instead of using an equivalent amount of DNA from a large prep.Starting with less than 10 cells and faithfully aliquoting all DNAensures uniform coverage in long fragments of any given region of thegenome. Starting with five or fewer cells allows four times or greatercoverage per each 100 kb DNA fragment in each aliquot without increasingthe total number of reads above 120 Gb (20 times coverage of a 6 Gbdiploid genome). However, a large number of aliquots (10,000 or more)and longer DNA fragments (>200 kb) can be of use when sequencing samplesobtained from a small number of cells, because for any given sequencethere are only as many overlapping fragments as the number of startingcells and the occurrence of overlapping fragments from both parentalchromosomes in an aliquot can be a devastating loss of information.

The LFR technology of the present invention is adapted to the problem ofsmall input DNA amounts, because it is effective with only about 10cells worth of starting input genomic DNA. In further embodiments, LFRis conducted on nucleic acids obtained from about 1-20, 2-18, 3-16,4-14, 5-12, 6-10, and 7-8 cells. In still further embodiments, LFR alsocan be used with nucleic acids obtained from a single cell, because thefirst step in LFR is generally a low bias whole genome amplificationwhich can be of particular use in single cell genomic analysis. Due toDNA strand breaks and DNA losses in handling, even single moleculesequencing methods would likely require some level of DNA amplificationfrom the single cell. The difficulty in sequencing single cells comesfrom trying to faithfully amplify the entire genome. Studies performedon bacteria using MDA have suffered from loss of approximately half ofthe genome in the final assembled sequence with a fairly high amount ofvariation in coverage across those sequenced regions. This can partiallybe explained as a result of the initial genomic DNA having nicks andstrand breaks which cannot be replicated at the ends and are thus lostduring the MDA process. In certain aspects, LFR provides a solution tothis problem, because it includes a step of generating long overlappingfragments of the genome prior to whole genome amplification methods suchas MDA. As is discussed in further detail above, these long fragmentsare in some embodiments generated using a gentle process for isolatingthe genomic DNA from the cell is used. The largely intact genomic DNA isthen lightly treated with a frequent nickase, resulting is a semirandomly nicked genome. The strand displacing ability of φ29 is thenused to polymerize from the nicks creating very long (>200 kb)overlapping fragments. These fragments are then be used as startingtemplate for the LFR process. In other embodiments, CoRE fragmentationtechniques as discussed above are used to generate long fragments priorto MDA. As will be appreciated, combinations of CoRE and other methodsknown in the art for generating fragments can also be utilized toprovide the materials for the steps of the LFR process described herein.

There are two basic approaches in advanced genome sequencing: usingamplified DNA or relying on single molecule detection. In general, thefirst group is expected to have lower costs of detection (higherthroughput) and the second group is expected to have lower cost in DNApreparation and reagents. To achieve accurate measurements, singlemolecule sequencing may require 100 times more measurements than usingamplified DNA due to non-synchronized base reads and/or longer detectiontimes. Alternatively, amplified DNA arrays have already demonstratedreduced reagent costs through miniaturization while still maintaininghigh quality low cost detection and further reagent reduction throughmicrofluidic devices is well within reach. As a result advancedminiaturized approaches that use amplified DNA are likely to be thefirst systems to provide low-cost medical genome sequencing.

For diagnostic medical applications low cost cannot compromise theaccuracy and completeness of the sequence. In addition to high per baseaccuracy, an important component of accuracy and completeness for humangenome sequencing is assembly of independent and accurate sequences ofboth parental chromosomes from diploid cells (including haplotype stateof methylation). This can be of importance for accurate predictions ofthe primary structure of synthesized protein or RNA alleles and theircorresponding levels of expression. Consensus sequence information isunable to make these predictions because enhancers and other sequencesresponsible for allelic expression levels can be over 100 kb upstream ofthe gene of interest or because two neighboring SNPs affecting the aminoacid sequence of a protein might reside on different alleles of the geneof interest.

To achieve chromosome level haplotyping, simulation experiments showthat allele linkage information across a range of at least 70-100 kb isneeded. This is impossible to achieve with technologies using amplifiedDNA. These technologies most likely would be limited to reads less than1000 bases due to difficulties in uniform amplification of long DNAmolecules and loss of linkage information in sequencing. Mate-pairtechnologies can provide an equivalent to the extended read length butare limited to less than 10 kb due to inefficiencies in making such DNAlibraries (i.e., circularization of DNA longer than a few kb is verydifficult). This approach also needs extreme read coverage to link allheterozygotes. An ideal technology for this would be single moleculesequencing of greater than 100 kb DNA fragments if processing such longmolecules were feasible and if the accuracy of single moleculesequencing were high and detection/instrument costs were low. This isvery difficult to achieve on short molecules with high yield let aloneon 100 kb fragments.

LFR provides a universal solution equivalent to inexpensive long singleDNA molecule sequencing that will make both current shorter readamplified DNA technologies and potential future longer read singlemolecule technologies less expensive to obtain and accurately assemblegenomic sequence data. At the same time this process will providecomplete haplotype resolution in complex diploid genomes and allows theassembly of metagenomic mixtures.

In one aspect, the present invention is based on virtual read lengths ofapproximately 100-1000 kb in length. In addition, LFR can alsodramatically reduce the computational demands and associated costs ofany short read technology. Importantly, LFR removes the need forextending sequencing read length if that reduces the overall yield.Combined with a low cost short read technology, such as DNA nanoarraybased cPAL (combinatorial probe anchor ligation) chemistry (describedfor example in published patent application numbers WO2007120208,WO2006073504, WO2007133831, and US2007099208, and U.S. patentapplication Ser. Nos. 11/679,124; 11/981,761; 11/981,661; 11/981,605;11/981,793; 11/981,804; 11/451,691; 11/981,607; 11/981,767; 11/982,467;11/451,692; 11/541,225; 11/927,356; 11/927,388; 11/938,096; 11/938,106;10/547,214; 11/981,730; 11/981,685; 11/981,797; 11/934,695; 11/934,697;11/934,703; 12/265,593; 11/938,213; 11/938,221; 12/325,922; 12/252,280;12/266,385; 12/329,365; 12/335,168; 12/335,188; and 12/361,507 all ofwhich are incorporated herein by reference in their entirety for allpurposes and in particular for all teachings related to sequencingtechnologies), LFR provides a complete solution for human genomesequencing at an affordable cost for medical and research applications.

LFR provides the ability to obtain actual sequences of individualchromosomes as opposed to just the consensus sequences of parental orrelated chromosomes (in spite of their high similarities and presence oflong repeats and segmental duplications). To generate this type of datathe continuity of sequence is in general established over long DNAranges such as 100 kb to 1 Mb. Traditionally such information wasobtained by BAC cloning, an expensive and unreliable process (e.g.,unclonable sequences). Most sequencing technologies generate relativelyshort DNA reads (100 to a few thousand bases). Furthermore, it is verydifficult to maintain long fragments in multiple processing steps. Thus,one advantage of LFR is that it provides a universal in-vitro process toobtain such information at a low cost.

LFR with 10,000 or more aliquots provides a large reduction in the costof computation incurred through short read length sequencingtechnologies and the complexity of genome assembly. This may be ofparticular importance for reducing the total cost of human genomesequencing below $1000.

LFR provides a reduction in the relatively high rate of errors orquestionable base calls, usually one in 100 kb or 30,000 false positivecalls and a similar number of undetected variants per human genome, thatplaque current genome sequencing technologies. To minimize follow upconfirmation of detected variants and to allow for adoption of humangenome sequencing for diagnostic applications such error rates can be10-1000 fold using methods of the present invention.

LFR using emulsion droplets is of particular use in reducing cost andincreasing efficiency. By reducing the total reaction volume of the LFRprocess by over 1000 fold, increasing the number of aliquots toapproximately 10,000, and improving the quality of data the total costof a complete genome processed via methods such as those describedherein and in published patent application numbers WO2007120208,WO2006073504, WO2007133831, and US2007099208, and U.S. patentapplication Ser. Nos. 11/679,124; 11/981,761; 11/981,661; 11/981,605;11/981,793; 11/981,804; 11/451,691; 11/981,607; 11/981,767; 11/982,467;11/451,692; 11/541,225; 11/927,356; 11/927,388; 11/938,096; 11/938,106;10/547,214; 11/981,730; 11/981,685; 11/981,797; 11/934,695; 11/934,697;11/934,703; 12/265,593; 11/938,213; 11/938,221; 12/325,922; 12/252,280;12/266,385; 12/329,365; 12/335,168; 12/335,188; and 12/361,507 all ofwhich are incorporated herein by reference in their entirety for allpurposes and in particular for all teachings related to sequencing andnucleic acid preparation, would be less than the 1,000 dollar mark.

In addition to being universal for all sequencing platforms, LFR basedsequencing can be applied beyond just standard personal genome analysisto all major applications of low cost-high throughput sequencing (e.g.,structural rearrangements in cancer genomes, full methylome analysisincluding the haplotypes of methylated sites, and de novo assemblyapplications for metagenomics or novel genome sequencing, even ofcomplex polyploid genomes like those found in plants).

Due to the universal nature and cost-effectiveness in providing linkedinformation for sequences separated by 100-1000 kb, this novel DNAprocessing and bar-coding technology is expected to have a broad andhighly beneficial impact on biosciences, medical genetics, and thedevelopment of new diagnostics and drugs; including novel treatments forcancer. One of the critical goals in various genomic applications is togenerate enough genome sequence data of high accuracy and completenessto be able to develop knowledge about various genome codes drivingcomplex genetic regulatory networks. The present invention encompassesLFR kits, tools and software for application to all genomics andsequencing platforms

LFR provides the ability to understand the genetic basis of thousands ofdiseases, especially for the large number of sporadic genetic diseases(with novel or combinatorial genetic defects) where only a few patientsare available to study. In these cases, the completeness of genomesequences (including complete haplotyping of all sequence variants andmethylation states) allows discovery of the actual genetic defects thatresult in such rare diseases.

In some embodiments, the present invention is of use in genetic medicaldiagnostics in cancer genomes and individual genomic sequencing.Complete sequencing of cancer genomes, in addition to helping to betterunderstand tumor development, will be critical for selecting optimalpersonalized cancer therapies. Accurate and complete sequence data at alow cost from a small number of cells may be of use in this importanthealth application. Second, individual genome sequencing for the purposeof personalized disease diagnoses, preventions, and treatments has to becomplete (full chromosomal haplotypes included), accurate and affordableto be effective. The present invention significantly improves all threemeasures of success. Such a low cost universal genetic test can beperformed as part of the in vitro fertilization process where only oneor two cells are available, as a prenatal diagnostic or a newborn screenand as part of routine health care for adults. Once implemented at animpact-achieving scale (over 10 million genomes sequenced per year) thisgenetic test could significantly reduce health care cost via preventivemeasures and appropriate drug use.

The present invention can yield haplotype reads in excess of 100 kb. Insome aspects, a cost reduction of approximately 10 fold can be achievedby reducing volumes to sub-microliter levels. This is achievable due tomethods, compositions and reaction conditions of the present inventionwhich allow the performance of all six enzymatic steps in the same wellwithout DNA purification. In some embodiments, the present inventionincludes the use of commercially available automated pipettingapproaches in 1536 well formats. Nanoliter (nl) dispensing tools (e.g.,Hamilton Robotics Nano Pipetting head, TTP LabTech Mosquito, and others)that provide non-contact pipetting of 50-100 nl can be used for fast andlow cost pipetting to make tens of genome libraries in parallel. Thefour fold increase in aliquots results in a large reduction in thecomplexity of the genome within each well reducing the overall cost ofcomputing over 10 fold and increasing data quality. Additionally, theautomation of this process increases the throughput and lower the handson cost of producing libraries.

In further embodiments, and as is discussed in further detail above,unique identification of each aliquot is achieved with barcode adaptortags. In embodiments utilizing multiwell plates, the same number ofadaptor tags as wells (384 and 1536 in two non-limiting examples) isused. In further embodiments, the costs associated with generatingadaptor tags is reduced through a novel combinatorial tagging approachbased on two sets of 40 half-barcode adapter tags.

A reduction of volumes down to picoliter levels in 10,000 aliquots canachieve an even greater cost reduction, possibly by as much as 30-400fold in reagent costs and an additional 10 fold (over 100 fold in total)in computational costs. In some embodiments, this level of costreduction and extensive aliquoting is accomplished through thecombination of the LFR process with combinatorial tagging to emulsion ormicrofluidic type devices. Again, one development in the presentinvention of conditions to perform all six enzymatic steps in the samereaction without DNA purification provides the ability ofminiaturization and automation, as well as adaptability to a widevariety of platforms and sample preparation methods.

Another advantage of LFR is that whole genome amplification can be muchmore efficient and show significantly less bias as a result of the smallvolumes and the long fragments used in LFR. Numerous studies haveexamined the range of unwanted amplification biases, background productformation, and chimeric artifacts introduced via φ29 based MDA, but manyof these shortcomings have occurred under extreme conditions ofamplification (greater than 1 million fold). LFR only needs a hundredthof that level of amplification. In addition, LFR starts with long DNAfragments (˜100 kb) which are critical for efficient MDA.

In one aspect, the present invention provides diploid genome sequencingtechniques that allow for calling parental haplotypes. LFR solves theproblem of determining parental haplotypes by separating correspondingparental DNA fragments of >100 kb in length into physically separatedsub-genome aliquots. As the number of aliquots increase, for instance to1536, and the percent of the genome decreases down to approximately 1%of a haploid genome, the statistical support for haplotypes increasesdramatically, because the sporadic presence of both maternal andpaternal haplotypes in the same well diminishes. Consequently, a largenumber of small aliquots with a negligent frequency of mixed haplotypesper aliquot allow the use of fewer cells. Similarly, longer fragments(e.g., 300 kb or longer) help bridge over segments lacking heterozygousloci.

An efficient algorithm for haplotyping can be made by calculating thepercent of shared aliquots (PSA) for a pair of neighboring alleles (FIG.29). This process resolves aliquots with mixed haplotypes or cases ofuncalled alleles in some aliquots. For 100 kb fragments from 20 cellsaliquoted in a 1536-well plate, the average PSA for pairs representingactual haplotypes reduces from close to 100% to 21% when the distancebetween neighboring heterozygous sites increases from 0 to 80 kb. ThePSA of the false haplotype pairs in rare cases (<1%) can represent 5-10%(1-2 out of 20 aliquots; approaching the PSA of 80 kb separated allelesin true haplotypes) due the random chance of two haplotypes existing inthe same aliquot. Thus, fragments even longer than 100 kb are requiredfor haplotyping neighboring heterozygous loci separated over 80 kb.

In one aspect, the methods and compositions of the present inventionprovide complete diploid genome sequencing technologies that allow forcalling polymorphic loci as homozygous. As a result of random sampling,there is a significant probability that at any given region of thegenome only one of the parental chromosomes has been sequenced. Anexpensive solution, and the one commonly employed in conventionalsequencing technologies, is to provide high average read coverage acrossthe entire genome. The present invention dramatically reduces thisproblem, because it requires much less sequence coverage than isrequired in conventional technologies. As one non-limiting example,consider a homozygous position in the human genome detected with fiveoverlapping reads (the reference in 99.9% of cases). If such positionsare declared homozygous the LFR method would be incorrect in one out of32 (each read provides a 0.5 probability of being correct, theprobability of being erroneous in all five cases is 0.5⁵ or 1/32) cases(˜3%), that is in 1/32 cases all 5 reads come from the same chromosomeand none from the other. Because of this it is usually preferred todeclare all of these positions as “no-call” or “half-call”. That leadsto millions of half-call positions per genome. If methods of the presentinvention (1536 or more aliquots) are used, 32/33 cases can berecognized as actual homozygous positions (some of the five reads comefrom aliquots of each parent) and only the remaining 3% would bedeclared half-calls (all reads come from aliquots of one parent). Toachieve this improvement the homozygous reference or SNP positions arecalled after haplotype phasing.

A similar advantage can be realized for reducing the false positive callrate. Most false calls have lower, but still sufficient coverage fromthe real second allele. Using LFR data, false positive cases can berecognized by determining that the better supported allele is present inaliquots from both parents. For example, a common situation encounteredin sequencing is a region covered by seven reads, five which correspondto A at a particular loci and two that correspond to G. If the two readsof G are false (e.g., mutations during DNA processing) they would mostlikely come from the same aliquot and five reads of A would come frommultiple aliquots belonging to both parents. This would indicatehomozygous A at the loci in question.

Mapping short reads to a reference genome, while less computationallycomplex than de novo sequencing, requires substantial computation,especially in cases where there are divergent or novel sequences createdby multiple mutations, insertions, and/or deletions. Such genomesegments require local or general de novo assembly of short sequencereads. Couple this with the reduction in reagent and imaging costs onnew generation DNA arrays having 3-6 billion spots per microscope slide(1-4 genomes per slide) and the computation effort for sequence assemblyrapidly becomes the dominate cost of genome sequencing. One way toreduce the costs associated with whole genome sequencing is to reducethese computation requirements.

The present invention provides LFR methods (>1500 aliquots) that providesolutions to the computational problem of short read sequencing atmultiple levels: (a) fast read mapping to the reference sequence, (b)minimizing number of loci that require extensive local assembly, and (c)orders of magnitude faster local and global de-novo assembly. This isachieved in part because by local assembly of less than 1% of the genomeat a time. In essence, the human genome assembly is reduced to theequivalent of 1000 bacterial genome assemblies. In one aspect, thefollowing sequence assembly process is used:

-   -   1. Map <1% of reads to entire genome reference.    -   2. Define 3-10 Mb (for 10,000 aliquots) of reference sequence        for each aliquot.    -   3. Map all reads from each aliquot to short aliquot reference.    -   4. Call ˜80% of the obvious heterozygous positions.    -   5. Establish parental chromosome haplotypes by phasing        heterozygous loci.    -   6. Call all homozygous reference (no variation) or SNPs and        short indels as well as low coverage heterozygous positions.    -   7. Define the sequences for the remaining ˜40K regions (1 in ˜1        million bases) that need extensive (including de novo) assembly.

By way of example for reducing mapping cost (a), consider the sequencingand mapping of DNA from five cells that has been divided into 10,000aliquots consisting of 0.1% of a haploid human genome per aliquot (3 Mbor thirty 100 kb fragments). If each aliquot was sequenced to four timescoverage with 120 base pair reads then there would be approximately100,000 reads per aliquot (3 Mb× 4/120). Each 100 kb fragment within analiquot would be covered by 3,300 reads. By mapping 500 (or 0.5%) of allreads in an aliquot against the entire human reference (step 1),amounting to approximately 15 reads per fragment, the reference segmentscorresponding to fragments in each aliquot will be defined (step 2). Theremaining reads would then be mapped to the 0.1-0.2% of the compositereference (3-6 Mb) uniquely defined for each aliquot (step 3). Thisprocess uses only 1% of the total mapping effort required without LFR ora 100 fold reduction in computation cost for mapping. In one embodiment,the present invention includes software for fast gathering and indexingof aliquot reference sequence.

The present invention improves the efficiency of diploid genomesequencing by first defining haplotypes (steps 4 and 5) and then usingaliquot-haplotype pairing to achieve accurate and computationallyefficient base (variant) calling for the majority of remaining cases(step 6). For example, for over almost 3 billion base positions in apersonal human genome there is a reference/reference homozygous state.Without LFR haplotype information on over 100 million positions cannotbe called at both chromosomes without extensive evaluation of novelsequences. With advanced LFR most of these positions can accurately bedetermined to be reference/reference without any de novo type sequenceassembly. This yields a computation reduction of approximately 1000 foldfor this genome assembly step. Furthermore, 99.9% of all variants in agenome (e.g., SNPs and 1-2 base indels) would be accurately called atthis step and the remaining 0.1% (forty thousand out of four millionvariants found per individual human genome), representing more complexchanges, would be solved in step 7.

Assuming a standard forty times coverage of a haploid genome (onebillion 120-base reads), a de novo assembly of sequence comprising anunresolved site in a parental chromosome (step 7), could be achievedusing approximately 100,000 reads (in about 10 of the 10,000 aliquots).This is much more efficient than using over 100 million (>10%) of theexpected unused reads in standard assembly without LFR. Additionally,false assembly is minimized even in the case of shorter overlap betweenconsecutive reads. Thus, a cost reduction in excess of 100 fold can beachieved per de novo assembly site.

The ability of LFR techniques of the present invention to sequence andassemble very long (>100 kb) fragments of the genome make it well suitedfor the sequencing of complete cancer genomes. It is has been suggestedthat more than 90% of cancers, in some manner, harbor significant lossesor gains in regions of the human genome, termed aneuploidy, with someindividual cancers having been observed to contain in excess of fourcopies of some chromosomes. This increased complexity in copy number ofchromosomes and regions within chromosomes can make sequencing usingmethods other than LFR untenable.

In further embodiments, the present invention utilizes automation tofurther reduce costs associated with whole genome sequencing. Themethods and compositions of the present invention also includeminiaturization, which can be achieved by a number of techniques,including the use of nanoliter-drops. In further embodiments, ˜10-20nanoliter drops are deposited in plates or on glass slides in 3072-6144format (still a cost effective total MDA volume of 60 μl without losingthe computational cost savings or the ability to sequence from fourcells) or higher using improved nano-pipetting or acoustic dropletejection technology (e.g., LabCyte Inc.) or using microfluidic devicescapable of handling up to 9216 individual reaction wells.

In one aspect, the present invention encompasses software with thecapability of handling data from in excess of 10,000 aliquots. Becausealiquot mapping is performed on a reference that is just a fewmegabases, a Smith-Waterman algorithm can be used instead of fastindexing that does not map reads with indels. This allows an accuratealignment of reads even to reference sequences with multiple changes orindels in a cost effective way.

III.B. Further Sequencing Methods

As will be appreciated, nucleic acids of the invention, includingfragments in LFR aliquot libraries and DNBs, can be used in anysequencing methods known in the art, including without limitationsequencing by ligation, sequencing by hybridization, sequencing bysynthesis (including sequencing by primer extension), chained sequencingby ligation of cleavable probes, and the like.

Methods similar to those described herein for sequencing can also beused to detect specific sequences in a target nucleic acid, includingdetection of single nucleotide polymorphisms (SNPs). In such methods,sequencing probes that will hybridize to a particular sequence, such asa sequence containing a SNP, can be used. Such sequencing probes can bedifferentially labeled to identify which SNP is present in the targetnucleic acid. Anchor probes can also be used in combination with suchsequencing probes to provide further stability and specificity.

In one aspect, methods and compositions of the present invention areused in combination with techniques such as those described inWO2007120208, WO2006073504, WO2007133831, and US2007099208, and U.S.Patent Application Nos. 60/992,485; 61/026,337; 61/035,914; 61/061,134;61/116,193; 61/102,586; Ser. Nos. 12/265,593; 12/266,385; 11/938,096;11/981,804; Nos. 11/981,797; 11/981,793; 11/981,767; 11/981,761;11/981,730; 11/981,685; 11/981,661; 11/981,607; 11/981,605; 11/927,388;11/927,356; 11/679,124; 11/541,225; 10/547,214; 11/451,692; and11/451,691, all of which are incorporated herein by reference in theirentirety for all purposes and in particular for all teachings related tosequencing, particularly sequencing of nucleic acids.

In a further aspect, sequences of nucleic acids are identified usingsequencing methods known in the art, including, but not limited to,hybridization-based methods, such as disclosed in Drmanac, U.S. Pat.Nos. 6,864,052; 6,309,824; and 6,401,267; and Drmanac et al, U.S. patentpublication 2005/0191656, and sequencing by synthesis methods, e.g.Nyren et al, U.S. Pat. No. 6,210,891; Ronaghi, U.S. Pat. No. 6,828,100;Ronaghi et al (1998), Science, 281: 363-365; Balasubramanian, U.S. Pat.No. 6,833,246; Quake, U.S. Pat. No. 6,911,345; Li et al, Proc. Natl.Acad. Sci. 100: 414-419 (2003); Smith et al, PCT publication WO2006/074351; and ligation-based methods, e.g. Shendure et al (2005),Science, 309: 1728-1739, Macevicz, U.S. Pat. No. 6,306,597, wherein eachof these references is herein incorporated by reference in its entiretyfor all purposes and in particular teachings regarding the figures,legends and accompanying text describing the compositions, methods ofusing the compositions and methods of making the compositions,particularly with respect to sequencing.

III.B.1. cPAL

Although the following is described in terms of sequencing DNBs, any ofthe sequencing methods described herein are also applicable to targetnucleic acid fragments, such as those generated for LFR sequencingmethods described above. As will be further appreciated, combinations ofsequencing methods are also encompassed by the present invention.

In one aspect, sequences of DNBs are identified using methods referredto herein as combinatorial probe anchor ligation (“cPAL”) and variationsthereof, as described below. In brief, cPAL involves identifying anucleotide at a particular detection position in a target nucleic acidby detecting a probe ligation product formed by ligation of at least oneanchor probe that hybridizes to all or part of an adaptor and asequencing probe that contains a particular nucleotide at an“interrogation position” that corresponds to (e.g. will hybridize to)the detection position. The sequencing probe contains a uniqueidentifying label. If the nucleotide at the interrogation position iscomplementary to the nucleotide at the detection position, ligation canoccur, resulting in a ligation product containing the unique label whichis then detected. Descriptions of different exemplary embodiments ofcPAL methods are provided below. It will be appreciated that thefollowing descriptions are not meant to be limiting and that variationsof the following embodiments are encompassed by the present invention.

“Complementary” or “substantially complementary” refers to thehybridization or base pairing or the formation of a duplex betweennucleotides or nucleic acids, such as, for instance, between the twostrands of a double-stranded DNA molecule or between an oligonucleotideprimer and a primer binding site on a single-stranded nucleic acid.Complementary nucleotides are, generally, A and T (or A and U), or C andG. Two single-stranded RNA or DNA molecules are said to be substantiallycomplementary when the nucleotides of one strand, optimally aligned andcompared and with appropriate nucleotide insertions or deletions, pairwith at least about 80% of the other strand, usually at least about 90%to about 95%, and even about 98% to about 100%.

As used herein, “hybridization” refers to the process in which twosingle-stranded polynucleotides bind non-covalently to form a stabledouble-stranded polynucleotide. The resulting (usually) double-strandedpolynucleotide is a “hybrid” or “duplex.” “Hybridization conditions”will typically include salt concentrations of less than about 1M, moreusually less than about 500 mM and may be less than about 200 mM. A“hybridization buffer” is a buffered salt solution such as 5% SSPE, orother such buffers known in the art. Hybridization temperatures can beas low as 5° C., but are typically greater than 22° C., and moretypically greater than about 30° C., and typically in excess of 37° C.Hybridizations are usually performed under stringent conditions, i.e.,conditions under which a probe will hybridize to its target subsequencebut will not hybridize to the other, uncomplimentary sequences.Stringent conditions are sequence-dependent and are different indifferent circumstances. For example, longer fragments may requirehigher hybridization temperatures for specific hybridization than shortfragments. As other factors may affect the stringency of hybridization,including base composition and length of the complementary strands,presence of organic solvents, and the extent of base mismatching, thecombination of parameters is more important than the absolute measure ofany one parameter alone. Generally stringent conditions are selected tobe about 5° C. lower than the T_(m) for the specific sequence at adefined ionic strength and pH. Exemplary stringent conditions include asalt concentration of at least 0.01M to no more than 1M sodium ionconcentration (or other salt) at a pH of about 7.0 to about 8.3 and atemperature of at least 25° C. For example, conditions of 5×SSPE (750 mMNaCl, 50 mM sodium phosphate, 5 mM EDTA at pH 7.4) and a temperature of30° C. are suitable for allele-specific probe hybridizations. Furtherexamples of stringent conditions are well known in the art, see forexample Sambrook J et al. (2001), Molecular Cloning, A LaboratoryManual, (3rd Ed., Cold Spring Harbor Laboratory Press.

As used herein, the term “T_(m)” generally refers to the temperature atwhich half of the population of double-stranded nucleic acid moleculesbecomes dissociated into single strands. The equation for calculatingthe Tm of nucleic acids is well known in the art. As indicated bystandard references, a simple estimate of the T_(m) value may becalculated by the equation: T_(m)=81.5+16.6(log10[Na+])0.41(%[G+C])−675/n−

-   1.0 m, when a nucleic acid is in aqueous solution having cation    concentrations of 0.5 M, or less, the (G+C) content is between 30%    and 70%, n is the number of bases, and m is the percentage of base    pair mismatches (see e.g., Sambrook J et al. (2001), Molecular    Cloning, A Laboratory Manual, (3rd Ed., Cold Spring Harbor    Laboratory Press). Other references include more sophisticated    computations, which take structural as well as sequence    characteristics into account for the calculation of T_(m) (see also,    Anderson and Young (1985), Quantitative Filter Hybridization,    Nucleic Acid Hybridization, and Allawi and SantaLucia (1997),    Biochemistry 36:10581-94).

In one example of a cPAL method, referred to herein as “single cPAL”, asillustrated in FIG. 23, anchor probe 2302 hybridizes to a complementaryregion on adaptor 2308 of the DNB 2301. Anchor probe 2302 hybridizes tothe adaptor region directly adjacent to target nucleic acid 2309, but insome cases, anchor probes can be designed to “reach into” the targetnucleic acid by incorporating a desired number of degenerate bases atthe terminus of the anchor probe, as is schematically illustrated inFIG. 24 and described further below. A pool of differentially labeledsequencing probes 2305 will hybridize to complementary regions of thetarget nucleic acid, and sequencing probes that hybridize adjacent toanchor probes are ligated to form a probe ligation product, usually byapplication of a ligase. The sequencing probes are generally sets orpools of oligonucleotides comprising two parts: different nucleotides atthe interrogation position, and then all possible bases (or a universalbase) at the other positions; thus, each probe represents each base typeat a specific position. The sequencing probes are labeled with adetectable label that differentiates each sequencing probe from thesequencing probes with other nucleotides at that position. Thus, in theexample illustrated in FIG. 23, a sequencing probe 2310 that hybridizesadjacent to anchor probe 2302 and is ligated to the anchor probe willidentify the base at a position in the target nucleic acid 5 bases fromthe adaptor as a “G”. FIG. 23 depicts a situation where theinterrogation base is 5 bases in from the ligation site, but as morefully described below, the interrogation base can also be “closer” tothe ligation site, and in some cases at the point of ligation. Onceligated, non-ligated anchor and sequencing probes are washed away, andthe presence of the ligation product on the array is detected using thelabel. Multiple cycles of anchor probe and sequencing probehybridization and ligation can be used to identify a desired number ofbases of the target nucleic acid on each side of each adaptor in a DNB.Hybridization of the anchor probe and the sequencing probe may occursequentially or simultaneously. The fidelity of the base call relies inpart on the fidelity of the ligase, which generally will not ligate ifthere is a mismatch close to the ligation site.

The present invention also provides methods in which two or more anchorprobes are used in every hybridization-ligation cycle. FIG. 25illustrate an additional example of a “double cPAL with overhang” methodin which a first anchor probe 2502 and a second anchor probe 2505 eachhybridize to complimentary regions of an adaptor. In the exampleillustrated in FIG. 25, the first anchor probe 2502 is fullycomplementary to a first region of the adaptor 2511, and the secondanchor probe 2505 is complementary to a second adaptor region adjacentto the hybridization position of the first anchor probe. The secondanchor probe also comprises degenerate bases at the terminus that is notadjacent to the first anchor probe. As a result, the second anchor probeis able to hybridize to a region of the target nucleic acid 2512adjacent to adaptor 2511 (the “overhang” portion). The second anchorprobe is generally too short to be maintained alone in its duplexhybridization state, but upon ligation to the first anchor probe itforms a longer anchor probe that is stably hybridized for subsequentmethods. As discussed above for the “single cPAL” method, a pool ofsequencing probes 2508 that represents each base type at a detectionposition of the target nucleic acid and labeled with a detectable labelthat differentiates each sequencing probe from the sequencing probeswith other nucleotides at that position is hybridized 2509 to theadaptor-anchor probe duplex and ligated to the terminal 5′ or 3′ base ofthe ligated anchor probes. In the example illustrated in FIG. 25, thesequencing probes are designed to interrogate the base that is fivepositions 5′ of the ligation point between the sequencing probe 2514 andthe ligated anchor probes 2513. Since the second adaptor probe 2505 hasfive degenerate bases at its 5′ end, it reaches five bases into thetarget nucleic acid 2512, allowing interrogation with the sequencingprobe at a full ten bases from the interface between the target nucleicacid 2512 and the adaptor 2511.

In variations of the above described examples of a double cPAL method,if the first anchor probe terminates closer to the end of the adaptor,the second adaptor probe will be proportionately more degenerate andtherefore will have a greater potential to not only ligate to the end ofthe first adaptor probe but also to ligate to other second adaptorprobes at multiple sites on the DNB. To prevent such ligation artifacts,the second anchor probes can be selectively activated to engage inligation to a first anchor probe or to a sequencing probe. Suchactivation methods are described in further detail below, and includemethods such as selectively modifying the termini of the anchor probessuch that they are able to ligate only to a particular anchor probe orsequencing probe in a particular orientation with respect to theadaptor.

Similar to the double cPAL method described above, it will beappreciated that cPAL methods utilizing three or more anchor probes arealso encompassed by the present invention.

In addition, sequencing reactions can be done at one or both of thetermini of each adaptor, e.g., the sequencing reactions can be“unidirectional” with detection occurring 3′ or 5′ of the adaptor or theother or the reactions can be “bidirectional” in which bases aredetected at detection positions 3′ and 5′ of the adaptor. Bidirectionalsequencing reactions can occur simultaneously—i.e., bases on both sidesof the adaptor are detected at the same time—or sequentially in anyorder.

Multiple cycles of cPAL (whether single, double, triple, etc.) willidentify multiple bases in the regions of the target nucleic acidadjacent to the adaptors. In brief, the cPAL methods are repeated forinterrogation of multiple adjacent bases within a target nucleic acid bycycling anchor probe hybridization and enzymatic ligation reactions withsequencing probe pools designed to detect nucleotides at varyingpositions removed from the interface between the adaptor and targetnucleic acid. In any given cycle, the sequencing probes used aredesigned such that the identity of one or more of bases at one or morepositions is correlated with the identity of the label attached to thatsequencing probe. Once the ligated sequencing probe (and hence thebase(s) at the interrogation position(s) is detected, the ligatedcomplex is stripped off of the DNB and a new cycle of adaptor andsequencing probe hybridization and ligation is conducted.

As will be appreciated, DNBs of the invention can be used in othersequencing methods in addition to the cPAL methods described above,including other sequencing by ligation methods as well as othersequencing methods, including without limitation sequencing byhybridization, sequencing by synthesis (including sequencing by primerextension), chained sequencing by ligation of cleavable probes, and thelike.

Methods similar to those described above for sequencing can also be usedto detect specific sequences in a target nucleic acid, includingdetection of single nucleotide polymorphisms (SNPs). In such methods,sequencing probes that will hybridize to a particular sequence, such asa sequence containing a SNP, will be applied. Such sequencing probes canbe differentially labeled to identify which SNP is present in the targetnucleic acid. Anchor probes can also be used in combination with suchsequencing probes to provide further stability and specificity.

Target nucleic acids of use in sequencing methods of the presentinvention comprise target sequences with a plurality of detectionpositions. The term “detection position” refers to a position in atarget sequence for which sequence information is desired. As will beappreciated by those in the art, generally a target sequence hasmultiple detection positions for which sequence information is required,for example in the sequencing of complete genomes as described herein.In some cases, for example in SNP analysis, it may be desirable to justread a single SNP in a particular area.

As discussed above, the present invention provides methods of sequencingthat utilize a combination of anchor probes and sequencing probes. By“sequencing probe” as used herein is meant an oligonucleotide that isdesigned to provide the identity of a nucleotide at a particulardetection position of a target nucleic acid. Sequencing probes hybridizeto domains within target sequences, e.g. a first sequencing probe mayhybridize to a first target domain, and a second sequencing probe mayhybridize to a second target domain. The terms “first target domain” and“second target domain” or grammatical equivalents herein means twoportions of a target sequence within a nucleic acid which is underexamination. The first target domain may be directly adjacent to thesecond target domain, or the first and second target domains may beseparated by an intervening sequence, for example an adaptor. The terms“first” and “second” are not meant to confer an orientation of thesequences with respect to the 5′-3′ orientation of the target sequence.For example, assuming a 5′-3′ orientation of the complementary targetsequence, the first target domain may be located either 5′ to the seconddomain, or 3′ to the second domain. Sequencing probes can overlap, e.g.a first sequencing probe can hybridize to the first 6 bases adjacent toone terminus of an adaptor, and a second sequencing probe can hybridizeto the 3rd-9th bases from the terminus of the adaptor (for example whenan anchor probe has three degenerate bases). Alternatively, a firstsequencing probe can hybridize to the 6 bases adjacent to the “upstream”terminus of an adaptor and a second sequencing probe can hybridize tothe 6 bases adjacent to the “downstream” terminus of an adaptor.

Sequencing probes will generally comprise a number of degenerate basesand a specific nucleotide at a specific location within the probe toquery the detection position (also referred to herein as an“interrogation position”).

In general, pools of sequencing probes are used when degenerate basesare used. That is, a probe having the sequence “NNNANN” is actually aset of probes of having all possible combinations of the four nucleotidebases at five positions (i.e., 1024 sequences) with an adenosine at the6th position, (As noted herein, this terminology is also applicable toadaptor probes: for example, when an adaptor probe has “three degeneratebases”, for example, it is actually a set of adaptor probes comprisingthe sequence corresponding to the anchor site, and all possiblecombinations at 3 positions, so it is a pool of 64 probes).

In some embodiments, for each interrogation position, four differentlylabeled pools can be combined in a single pool and used in a sequencingstep. Thus, in any particular sequencing step, 4 pools are used, eachwith a different specific base at the interrogation position and with adifferent label corresponding to the base at the interrogation position.That is, sequencing probes are also generally labeled such that aparticular nucleotide at a particular interrogation position isassociated with a label that is different from the labels of sequencingprobes with a different nucleotide at the same interrogation position.For example, four pools can be used: NNNANN-dye1, NNNTNN-dye2,NNNCNN-dye3 and NNNGNN-dye4 in a single step, as long as the dyes areoptically resolvable. In some embodiments, for example for SNPdetection, it may only be necessary to include two pools, as the SNPcall will be either a C or an A, etc. Similarly, some SNPs have threepossibilities. Alternatively, in some embodiments, if the reactions aredone sequentially rather than simultaneously, the same dye can be done,just in different steps: e.g. the NNNANN-dye1 probe can be used alone ina reaction, and either a signal is detected or not, and the probeswashed away; then a second pool, NNNTNN-dye1 can be introduced.

In any of the sequencing methods described herein, sequencing probes mayhave a wide range of lengths, including about 3 to about 25 bases. Infurther embodiments, sequencing probes may have lengths in the range ofabout 5 to about 20, about 6 to about 18, about 7 to about 16, about 8to about 14, about 9 to about 12, and about 10 to about 11 bases.

Sequencing probes of the present invention are designed to becomplementary, and in general, perfectly complementary, to a sequence ofthe target sequence such that hybridization of a portion target sequenceand probes of the present invention occurs. In particular, it isimportant that the interrogation position base and the detectionposition base be perfectly complementary and that the methods of theinvention do not result in signals unless this is true.

In many embodiments, sequencing probes are perfectly complementary tothe target sequence to which they hybridize; that is, the experimentsare run under conditions that favor the formation of perfect basepairing, as is known in the art. As will be appreciated by those in theart, a sequencing probe that is perfectly complementary to a firstdomain of the target sequence could be only substantially complementaryto a second domain of the same target sequence; that is, the presentinvention relies in many cases on the use of sets of probes, forexample, sets of hexamers, that will be perfectly complementary to sometarget sequences and not to others.

In some embodiments, depending on the application, the complementaritybetween the sequencing probe and the target need not be perfect; theremay be any number of base pair mismatches, which will interfere withhybridization between the target sequence and the single strandednucleic acids of the present invention. However, if the number ofmismatches is so great that no hybridization can occur under even theleast stringent of hybridization conditions, the sequence is not acomplementary target sequence. Thus, by “substantially complementary”herein is meant that the sequencing probes are sufficientlycomplementary to the target sequences to hybridize under normal reactionconditions. However, for most applications, the conditions are set tofavor probe hybridization only if perfectly complementarity exists.Alternatively, sufficient complementarity is required to allow theligase reaction to occur; that is, there may be mismatches in some partof the sequence but the interrogation position base should allowligation only if perfect complementarity at that position occurs.

In some cases, in addition to or instead of using degenerate bases inprobes of the invention, universal bases which hybridize to more thanone base can be used. For example, inosine can be used. Any combinationof these systems and probe components can be utilized.

Sequencing probes of use in methods of the present invention are usuallydetectably labeled. By “label” or “labeled” herein is meant that acompound has at least one element, isotope or chemical compound attachedto enable the detection of the compound. In general, labels of use inthe invention include without limitation isotopic labels, which may beradioactive or heavy isotopes, magnetic labels, electrical labels,thermal labels, colored and luminescent dyes, enzymes and magneticparticles as well. Dyes of use in the invention may be chromophores,phosphors or fluorescent dyes, which due to their strong signals providea good signal-to-noise ratio for decoding. Sequencing probes may also belabeled with quantum dots, fluorescent nanobeads or other constructsthat comprise more than one molecule of the same fluorophore. Labelscomprising multiple molecules of the same fluorophore will generallyprovide a stronger signal and will be less sensitive to quenching thanlabels comprising a single molecule of a fluorophore. It will beunderstood that any discussion herein of a label comprising afluorophore will apply to labels comprising single and multiplefluorophore molecules.

Many embodiments of the invention include the use of fluorescent labels.Suitable dyes for use in the invention include, but are not limited to,fluorescent lanthanide complexes, including those of Europium andTerbium, fluorescein, rhodamine, tetramethylrhodamine, eosin,erythrosin, coumarin, methyl-coumarins, pyrene, Malacite green,stilbene, Lucifer Yellow, Cascade Blue™, Texas Red, and others describedin the 6th Edition of the Molecular Probes Handbook by Richard P.Haugland, hereby expressly incorporated by reference in its entirety forall purposes and in particular for its teachings regarding labels of usein accordance with the present invention. Commercially availablefluorescent dyes for use with any nucleotide for incorporation intonucleic acids include, but are not limited to: Cy3, Cy5, (AmershamBiosciences, Piscataway, N.J., USA), fluorescein, tetramethylrhodamine-,Texas Red®, Cascade Blue®, BODIPY® FL-14, BODIPY®R, BODIPY® TR-14,Rhodamine Green™, Oregon Green® 488, BODIPY® 630/650, BODIPY® 650/665-,Alexa Fluor® 488, Alexa Fluor® 532, Alexa Fluor® 568, Alexa Fluor® 594,Alexa Fluor® 546 (Molecular Probes, Inc. Eugene, Oreg., USA), Quasar570, Quasar 670, Cal Red 610 (BioSearch Technologies, Novato, Ca). Otherfluorophores available for post-synthetic attachment include, interalia, Alexa Fluor® 350, Alexa Fluor® 532, Alexa Fluor® 546, Alexa Fluor®568, Alexa Fluor® 594, Alexa Fluor® 647, BODIPY 493/503, BODIPY FL,BODIPY R6G, BODIPY 530/550, BODIPY TMR, BODIPY 558/568, BODIPY 558/568,BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY 630/650, BODIPY650/665, Cascade Blue, Cascade Yellow, Dansyl, lissamine rhodamine B,Marina Blue, Oregon Green 488, Oregon Green 514, Pacific Blue, rhodamine6G, rhodamine green, rhodamine red, tetramethylrhodamine, Texas Red(available from Molecular Probes, Inc., Eugene, Oreg., USA), and Cy2,Cy3.5, Cy5.5, and Cy7 (Amersham Biosciences, Piscataway, N.J. USA, andothers). In some embodiments, the labels used include fluoroscein, Cy3,Texas Red, Cy5, Quasar 570, Quasar 670 and Cal Red 610 are used inmethods of the present invention.

Labels can be attached to nucleic acids to form the labeled sequencingprobes of the present invention using methods known in the art, and to avariety of locations of the nucleosides. For example, attachment can beat either or both termini of the nucleic acid, or at an internalposition, or both. For example, attachment of the label may be done on aribose of the ribose-phosphate backbone at the 2′ or 3′ position (thelatter for use with terminal labeling), in one embodiment through anamide or amine linkage. Attachment may also be made via a phosphate ofthe ribose-phosphate backbone, or to the base of a nucleotide. Labelscan be attached to one or both ends of a probe or to any one of thenucleotides along the length of a probe.

Sequencing probes are structured differently depending on theinterrogation position desired. For example, in the case of sequencingprobes labeled with fluorophores, a single position within eachsequencing probe will be correlated with the identity of the fluorophorewith which it is labeled. Generally, the fluorophore molecule will beattached to the end of the sequencing probe that is opposite to the endtargeted for ligation to the anchor probe.

By “anchor probe” as used herein is meant an oligonucleotide designed tobe complementary to at least a portion of an adaptor, referred to hereinas “an anchor site”. Adaptors can contain multiple anchor sites forhybridization with multiple anchor probes, as described herein. Asdiscussed further herein, anchor probes of use in the present inventioncan be designed to hybridize to an adaptor such that at least one end ofthe anchor probe is flush with one terminus of the adaptor (either“upstream” or “downstream”, or both). In further embodiments, anchorprobes can be designed to hybridize to at least a portion of an adaptor(a first adaptor site) and also at least one nucleotide of the targetnucleic acid adjacent to the adaptor (“overhangs”). As illustrated inFIG. 24, anchor probe 2402 comprises a sequence complementary to aportion of the adaptor. Anchor probe 2402 also comprises four degeneratebases at one terminus. This degeneracy allows for a portion of theanchor probe population to fully or partially match the sequence of thetarget nucleic acid adjacent to the adaptor and allows the anchor probeto hybridize to the adaptor and reach into the target nucleic acidadjacent to the adaptor regardless of the identity of the nucleotides ofthe target nucleic acid adjacent to the adaptor. This shift of theterminal base of the anchor probe into the target nucleic acid shiftsthe position of the base to be called closer to the ligation point, thusallowing the fidelity of the ligase to be maintained. In general,ligases ligate probes with higher efficiency if the probes are perfectlycomplementary to the regions of the target nucleic acid to which theyare hybridized, but the fidelity of ligases decreases with distance awayfrom the ligation point. Thus, in order to minimize and/or preventerrors due to incorrect pairing between a sequencing probe and thetarget nucleic acid, it can be useful to maintain the distance betweenthe nucleotide to be detected and the ligation point of the sequencingand anchor probes. By designing the anchor probe to reach into thetarget nucleic acid, the fidelity of the ligase is maintained whilestill allowing a greater number of nucleotides adjacent to each adaptorto be identified. Although the embodiment illustrated in FIG. 24 is onein which the sequencing probe hybridizes to a region of the targetnucleic acid on one side of the adaptor, it will be appreciated thatembodiments in which the sequencing probe hybridizes on the other sideof the adaptor are also encompassed by the invention. In FIG. 24, “N”represents a degenerate base and “B” represents nucleotides ofundetermined sequence. As will be appreciated, in some embodiments,rather than degenerate bases, universal bases may be used.

Anchor probes of the invention may comprise any sequence that allows theanchor probe to hybridize to a DNB, generally to an adaptor of a DNB.Such anchor probes may comprise a sequence such that when the anchorprobe is hybridized to an adaptor, the entire length of the anchor probeis contained within the adaptor. In some embodiments, anchor probes maycomprise a sequence that is complementary to at least a portion of anadaptor and also comprise degenerate bases that are able to hybridize totarget nucleic acid regions adjacent to the adaptor. In some exemplaryembodiments, anchor probes are hexamers that comprise 3 bases that arecomplementary to an adaptor and 3 degenerate bases. In some exemplaryembodiments, anchor probes are 8-mers that comprise 3 bases that arecomplementary to an adaptor and 5 degenerate bases. In further exemplaryembodiments, particularly when multiple anchor probes are used, a firstanchor probe comprises a number of bases complementary to an adaptor atone end and degenerate bases at another end, whereas a second anchorprobe comprises all degenerate bases and is designed to ligate to theend of the first anchor probe that comprises degenerate bases. It willbe appreciated that these are exemplary embodiments, and that a widerange of combinations of known and degenerate bases can be used toproduce anchor probes of use in accordance with the present invention.

In certain aspects, the sequencing by ligation methods of the inventioninclude providing different combinations of anchor probes and sequencingprobes, which, when hybridized to adjacent regions on a DNB, can beligated to form probe ligation products. The probe ligation products arethen detected, which provides the identity of one or more nucleotides inthe target nucleic acid. By “ligation” as used herein is meant anymethod of joining two or more nucleotides to each other. Ligation caninclude chemical as well as enzymatic ligation. In general, thesequencing by ligation methods discussed herein utilize enzymaticligation by ligases. Such ligases invention can be the same or differentthan ligases discussed above for creation of the nucleic acid templates.Such ligases include without limitation DNA ligase 1, DNA ligase II, DNAligase III, DNA ligase IV, E. coli DNA ligase, T4 DNA ligase, T4 RNAligase 1, T4 RNA ligase 2, T7 ligase, T3 DNA ligase, and thermostableligases (including without limitation Taq ligase) and the like. Asdiscussed above, sequencing by ligation methods often rely on thefidelity of ligases to only join probes that are perfectly complementaryto the nucleic acid to which they are hybridized. This fidelity willdecrease with increasing distance between a base at a particularposition in a probe and the ligation point between the two probes. Assuch, conventional sequencing by ligation methods can be limited in thenumber of bases that can be identified. The present invention increasesthe number of bases that can be identified by using multiple probepools, as is described further herein.

A variety of hybridization conditions may be used in the sequencing byligation methods of sequencing as well as other methods of sequencingdescribed herein. These conditions include high, moderate and lowstringency conditions; see for example Maniatis et al., MolecularCloning: A Laboratory Manual, 2d Edition, 1989, and Short Protocols inMolecular Biology, ed. Ausubel, et al, which are hereby incorporated byreference. Stringent conditions are sequence-dependent and will bedifferent in different circumstances. Longer sequences hybridizespecifically at higher temperatures. An extensive guide to thehybridization of nucleic acids is found in Tijssen, Techniques inBiochemistry and Molecular Biology—Hybridization with Nucleic AcidProbes, “Overview of principles of hybridization and the strategy ofnucleic acid assays,” (1993). Generally, stringent conditions areselected to be about 5-10° C. lower than the thermal melting point (Tm)for the specific sequence at a defined ionic strength and pH. The Tm isthe temperature (under defined ionic strength, pH and nucleic acidconcentration) at which 50% of the probes complementary to the targethybridize to the target sequence at equilibrium (as the target sequencesare present in excess, at Tm, 50% of the probes are occupied atequilibrium). Stringent conditions can be those in which the saltconcentration is less than about 1.0 M sodium ion, typically about 0.01to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 andthe temperature is at least about 30° C. for short probes (e.g. 10 to 50nucleotides) and at least about 60° C. for long probes (e.g. greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of helix destabilizing agents such as formamide. Thehybridization conditions may also vary when a non-ionic backbone, i.e.PNA is used, as is known in the art. In addition, cross-linking agentsmay be added after target binding to cross-link, i.e. covalently attach,the two strands of the hybridization complex.

For any of sequencing methods known in the art and described hereinusing nucleic acids of the invention (including LFR aliquot fragmentsand DNBs), the present invention provides methods for determining atleast about 10 to about 200 bases in target nucleic acids. In furtherembodiments, the present invention provides methods for determining atleast about 20 to about 180, about 30 to about 160, about 40 to about140, about 50 to about 120, about 60 to about 100, and about 70 to about80 bases in target nucleic acids. In still further embodiments,sequencing methods are used to identify at least 5, 10, 15, 20, 25, 30or more bases adjacent to one or both ends of each adaptor in a nucleicacid template of the invention.

Any of the sequencing methods described herein and known in the art canbe applied to nucleic acids in solution or on a surface and/or in anarray.

III.B.1(a) Single cPAL

In one aspect, the present invention provides methods for identifyingsequences of DNBs by using combinations of sequencing and anchor probesthat hybridize to adjacent regions of a DNB and are ligated, usually byapplication of a ligase. Such methods are generally referred to hereinas cPAL (combinatorial probe anchor ligation) methods. In one aspect,cPAL methods of the invention produce probe ligation products comprisinga single anchor probe and a single sequencing probe. Such cPAL methodsin which only a single anchor probe is used are referred to herein as“single cPAL”.

One embodiment of single cPAL is illustrated in FIG. 23. A monomericunit 2301 of a DNB comprises a target nucleic acid 2309 and an adaptor2308. An anchor probe 2302 hybridizes to a complementary region onadaptor 2308. In the example illustrated in FIG. 23, anchor probe 2302hybridizes to the adaptor region directly adjacent to target nucleicacid 2309, although, as is discussed further herein, anchor probes canalso be designed to reach into the target nucleic acid adjacent to anadaptor by incorporating a desired number of degenerate bases at theterminus of the anchor probe. A pool of differentially labeledsequencing probes 2306 will hybridize to complementary regions of thetarget nucleic acid. A sequencing probe 2310 that hybridizes to theregion of target nucleic acid 2309 adjacent to anchor probe 2302 will beligated to the anchor probe form a probe ligation product. Theefficiency of hybridization and ligation is increased when the base inthe interrogation position of the probe is complementary to the unknownbase in the detection position of the target nucleic acid. Thisincreased efficiency favors ligation of perfectly complementarysequencing probes to anchor probes over mismatch sequencing probes. Asdiscussed above, ligation is generally accomplished enzymatically usinga ligase, but other ligation methods can also be utilized in accordancewith the invention. In FIG. 23, “N” represents a degenerate base and “B”represents nucleotides of undetermined sequence. As will be appreciated,in some embodiments, rather than degenerate bases, universal bases maybe used.

As also discussed above, the sequencing probes can be oligonucleotidesrepresenting each base type at a specific position and labeled with adetectable label that differentiates each sequencing probe from thesequencing probes with other nucleotides at that position. Thus, in theexample illustrated in FIG. 23, a sequencing probe 2310 that hybridizesadjacent to anchor probe 2302 and is ligated to the anchor probe willidentify the base at a position in the target nucleic acid 5 bases fromthe adaptor as a “G”. Multiple cycles of anchor probe and sequencingprobe hybridization and ligation can be used to identify a desirednumber of bases of the target nucleic acid on each side of each adaptorin a DNB.

As will be appreciated, hybridization of the anchor probe and thesequencing probe can be sequential or simultaneous in any of the cPALmethods described herein.

In the embodiment illustrated in FIG. 23, sequencing probe 2310hybridizes to a region “upstream” of the adaptor, however it will beappreciated that sequencing probes may also hybridize “downstream” ofthe adaptor. The terms “upstream” and “downstream” refer to the regions5′ and 3′ of the adaptor, depending on the orientation of the system. Ingeneral, “upstream” and “downstream” are relative terms and are notmeant to be limiting; rather they are used for ease of understanding. Asillustrated in FIG. 6, a sequencing probe 607 can hybridize downstreamof adaptor 604 to identify a nucleotide 4 bases away from the interfacebetween the adaptor and the target nucleic acid 603. In furtherembodiments, sequencing probes can hybridize both upstream anddownstream of the adaptor to identify nucleotides at positions in thenucleic acid on both sides of the adaptor. Such embodiments allowgeneration of multiple points of data from each adaptor for eachhybridization-ligation-detection cycle of the single cPAL method.

In some embodiments, probes used in a single cPAL method may have fromabout 3 to about 20 bases corresponding to an adaptor and from about 1to about 20 degenerate bases (i.e., in a pool of anchor probes). Suchanchor probes may also include universal bases, as well as combinationsof degenerate and universal bases.

In some embodiments, anchor probes with degenerated bases may have about1-5 mismatches with respect to the adaptor sequence to increase thestability of full match hybridization at the degenerated bases. Such adesign provides an additional way to control the stability of theligated anchor and sequencing probes to favor those probes that areperfectly matched to the target (unknown) sequence. In furtherembodiments, a number of bases in the degenerate portion of the anchorprobes may be replaced with abasic sites (i.e., sites which do not havea base on the sugar) or other nucleotide analogs to influence thestability of the hybridized probe to favor the full match hybrid at thedistal end of the degenerate part of the anchor probe that willparticipate in the ligation reactions with the sequencing probes, asdescribed herein. Such modifications may be incorporated, for example,at interior bases, particularly for anchor probes that comprise a largenumber (i.e., greater than 5) of degenerated bases. In addition, some ofthe degenerated or universal bases at the distal end of the anchor probemay be designed to be cleavable after hybridization (for example byincorporation of a uracil) to generate a ligation site to the sequencingprobe or to a second anchor probe, as described further below.

In further embodiments, the hybridization of the anchor probes can becontrolled through manipulation of the reaction conditions, for examplethe stringency of hybridization. In an exemplary embodiment, the anchorhybridization process may start with conditions of high stringency(higher temperature, lower salt, higher pH, higher concentration offormamide, and the like), and these conditions may be gradually orstepwise relaxed. This may require consecutive hybridization cycles inwhich different pools of anchor probes are removed and then added insubsequent cycles. Such methods provide a higher percentage of targetnucleic acid occupied with perfectly complementary anchor probes,particularly anchor probes perfectly complementary at positions at thedistal end that will be ligated to the sequencing probe. Hybridizationtime at each stringency condition may also be controlled to obtaingreater numbers of full match hybrids.

III.B.1(b) Double cPAL (and Beyond)

In still further embodiments, the present invention provides cPALmethods utilizing two ligated anchor probes in everyhybridization-ligation cycle. See for example U.S. Patent ApplicationSer. Nos. 60/992,485; 61/026,337; 61/035,914 and 61/061,134, which arehereby expressly incorporated by reference in their entirety, andespecially the examples and claims. FIG. 25 illustrates an example of a“double cPAL” method in which a first anchor probe 2502 and a secondanchor probe 2505 hybridize to complimentary regions of an adaptor; thatis, the first anchor probe hybridizes to the first anchor site and thesecond anchor probe hybridizes to the second adaptor site. In theexample illustrated in FIG. 25, the first anchor probe 2502 is fullycomplementary to a region of the adaptor 2511 (the first anchor site),and the second anchor probe 2505 is complementary to the adaptor regionadjacent to the hybridization position of the first anchor probe (thesecond anchor site). In general, the first and second anchor sites areadjacent.

The second anchor probe may optionally also comprises degenerate basesat the terminus that is not adjacent to the first anchor probe such thatit will hybridize to a region of the target nucleic acid 2512 adjacentto adaptor 2511. This allows sequence information to be generated fortarget nucleic acid bases farther away from the adaptor/targetinterface. Again, as outlined herein, when a probe is said to have“degenerate bases”, it means that the probe actually comprises a set ofprobes, with all possible combinations of sequences at the degeneratepositions. For example, if an anchor probe is 9 bases long with 6 knownbases and three degenerate bases, the anchor probe is actually a pool of64 probes.

The second anchor probe is generally too short to be maintained alone inits duplex hybridization state, but upon ligation to the first anchorprobe it forms a longer anchor probe that is stable for subsequentmethods. In the some embodiments, the second anchor probe has about 1 toabout 5 bases that are complementary to the adaptor and about 5 to about10 bases of degenerate sequence. As discussed above for the “singlecPAL” method, a pool of sequencing probes 2508 representing each basetype at a detection position of the target nucleic acid and labeled witha detectable label that differentiates each sequencing probe from thesequencing probes with other nucleotides at that position is hybridized2509 to the adaptor-anchor probe duplex and ligated to the terminal 5′or 3′ base of the ligated anchor probes. In the example illustrated inFIG. 25, the sequencing probes are designed to interrogate the base thatis five positions 5′ of the ligation point between the sequencing probe2514 and the ligated anchor probes 2513. Since the second anchor probe2505 has five degenerate bases at its 5′ end, it reaches 5 bases intothe target nucleic acid 2512, allowing interrogation with the sequencingprobe at a full 10 bases from the interface between the target nucleicacid 2512 and the adaptor 2511. In FIG. 25, “N” represents a degeneratebase and “B” represents nucleotides of undetermined sequence. As will beappreciated, in some embodiments, rather than degenerate bases,universal bases may be used.

In some embodiments, the second anchor probe may have about 5-10 basescorresponding to an adaptor and about 5-15 bases, which are generallydegenerated, corresponding to the target nucleic acid. This secondanchor probe may be hybridized first under optimal conditions to favorhigh percentages of target occupied with full match at a few basesaround the ligation point between the two anchor probes. The firstadaptor probe and/or the sequencing probe may be hybridized and ligatedto the second anchor probe in a single step or sequentially. In someembodiments, the first and second anchor probes may have at theirligation point from about 5 to about 50 complementary bases that are notcomplementary to the adaptor, thus forming a “branching-out” hybrid.This design allows an adaptor-specific stabilization of the hybridizedsecond anchor probe. In some embodiments, the second anchor probe isligated to the sequencing probe before hybridization of the first anchorprobe; in some embodiments the second anchor probe is ligated to thefirst anchor probe prior to hybridization of the sequencing probe; insome embodiments the first and second anchor probes and the sequencingprobe hybridize simultaneously and ligation occurs between the first andsecond anchor probe and between the second anchor probe and thesequencing probe simultaneously or essentially simultaneously, while inother embodiments the ligation between the first and second anchor probeand between the second anchor probe and the sequencing probe occurssequentially in any order. Stringent washing conditions can be used toremove unligated probes; (e.g., using temperature, pH, salt, a bufferwith an optimal concentration of formamide can all be used, with optimalconditions and/or concentrations being determined using methods known inthe art). Such methods can be particularly useful in methods utilizingsecond anchor probes with large numbers of degenerated bases that arehybridized outside of the corresponding junction point between theanchor probe and the target nucleic acid.

In certain embodiments, double cPAL methods utilize ligation of twoanchor probes in which one anchor probe is fully complementary to anadaptor and the second anchor probe is fully degenerate (again, actuallya pool of probes). An example of such a double cPAL method isillustrated in FIG. 26, in which the first anchor probe 2602 ishybridized to adaptor 2611 of DNB 2601. The second anchor probe 2605 isfully degenerate and is thus able to hybridize to the unknownnucleotides of the region of the target nucleic acid 2612 adjacent toadaptor 2611. The second anchor probe is designed to be too short to bemaintained alone in its duplex hybridization state, but upon ligation tothe first anchor probe the formation of the longer ligated anchor probeconstruct provides the stability needed for subsequent steps of the cPALprocess. The second fully degenerate anchor probe may in someembodiments be from about 5 to about 20 bases in length. For longerlengths (i.e., above 10 bases), alterations to hybridization andligation conditions may be introduced to lower the effective Tm of thedegenerate anchor probe. The shorter second anchor probe will generallybind non-specifically to target nucleic acid and adaptors, but itsshorter length will affect hybridization kinetics such that in generalonly those second anchor probes that are perfectly complementary toregions adjacent to the adaptors and the first anchor probes will havethe stability to allow the ligase to join the first and second anchorprobes, generating the longer ligated anchor probe construct.Non-specifically hybridized second anchor probes will not have thestability to remain hybridized to the DNB long enough to subsequently beligated to any adjacently hybridized sequencing probes. In someembodiments, after ligation of the second and first anchor probes, anyunligated anchor probes will be removed, usually by a wash step. In FIG.26, “N” represents a degenerate base and “B” represents nucleotides ofundetermined sequence. As will be appreciated, in some embodiments,rather than degenerate bases, universal bases may be used.

In further exemplary embodiments, the first anchor probe will be ahexamer comprising 3 bases complementary to the adaptor and 3 degeneratebases, whereas the second anchor probe comprises only degenerate basesand the first and second anchor probes are designed such that only theend of the first anchor probe with the degenerate bases will ligate tothe second anchor probe. In further exemplary embodiments, the firstanchor probe is an 8-mer comprising 3 bases complementary to an adaptorand 5 degenerate bases, and again the first and second anchor probes aredesigned such that only the end of the first anchor probe with thedegenerate bases will ligate to the second anchor probe. It will beappreciated that these are exemplary embodiments and that a wide rangeof combinations of known and degenerate bases can be used in the designof both the first and second (and in some embodiments the third and/orfourth) anchor probes.

In variations of the above described examples of a double cPAL method,if the first anchor probe terminates closer to the end of the adaptor,the second anchor probe will be proportionately more degenerate andtherefore will have a greater potential to not only ligate to the end ofthe first anchor probe but also to ligate to other second anchor probesat multiple sites on the DNB. To prevent such ligation artifacts, thesecond anchor probes can be selectively activated to engage in ligationto a first anchor probe or to a sequencing probe. Such activationinclude selectively modifying the termini of the anchor probes such thatthey are able to ligate only to a particular anchor probe or sequencingprobe in a particular orientation with respect to the adaptor. Forexample, 5′ and 3′ phosphate groups can be introduced to the secondanchor probe, with the result that the modified second anchor probewould be able to ligate to the 3′ end of a first anchor probe hybridizedto an adaptor, but two second anchor probes would not be able to ligateto each other (because the 3′ ends are phosphorylated, which wouldprevent enzymatic ligation). Once the first and second anchor probes areligated, the 3′ ends of the second anchor probe can be activated byremoving the 3′ phosphate group (for example with T4 polynucleotidekinase or phosphatases such as shrimp alkaline phosphatase and calfintestinal phosphatase).

If it is desired that ligation occur between the 3′ end of the secondanchor probe and the 5′ end of the first anchor probe, the first anchorprobe can be designed and/or modified to be phosphorylated on its 5′ endand the second anchor probe can be designed and/or modified to have no5′ or 3′ phosphorylation. Again, the second anchor probe would be ableto ligate to the first anchor probe, but not to other second anchorprobes. Following ligation of the first and second anchor probes, a 5′phosphate group can be produced on the free terminus of the secondanchor probe (for example, by using T4 polynucleotide kinase) to make itavailable for ligation to sequencing probes in subsequent steps of thecPAL process.

In some embodiments, the two anchor probes are applied to the DNBssimultaneously. In some embodiments, the two anchor probes are appliedto the DNBs sequentially, allowing one of the anchor probes to hybridizeto the DNBs before the other. In some embodiments, the two anchor probesare ligated to each other before the second adaptor is ligated to thesequencing probe. In some embodiments, the anchor probes and thesequencing probe are ligated in a single step. In embodiments in whichtwo anchor probes and the sequencing probe are ligated in a single step,the second adaptor can be designed to have enough stability to maintainits position until all three probes (the two anchor probes and thesequencing probe) are in place for ligation. For example, a secondanchor probe comprising five bases complementary to the adaptor and fivedegenerate bases for hybridization to the region of the target nucleicacid adjacent to the adaptor can be used. Such a second anchor probe mayhave sufficient stability to be maintained with low stringency washing,and thus a ligation step would not be necessary between the steps ofhybridization of the second anchor probe and hybridization of asequencing probe. In the subsequent ligation of the sequencing probe tothe second anchor probe, the second anchor probe would also be ligatedto the first anchor probe, resulting in a duplex with increasedstability over any of the anchor probes or sequencing probes alone.

Similar to the double cPAL method described above, it will beappreciated that cPAL with three or more anchor probes is alsoencompassed by the present invention. Such anchor probes can be designedin accordance with methods described herein and known in the art tohybridize to regions of adaptors such that one terminus of one of theanchor probes is available for ligation to sequencing probes hybridizedadjacent to the terminal anchor probe. In an exemplary embodiment, threeanchor probes are provided—two are complementary to different sequenceswithin an adaptor and the third comprises degenerate bases to hybridizeto sequences within the target nucleic acid. In a further embodiment,one of the two anchors complementary to sequences within the adaptor mayalso comprise one or more degenerate bases at on terminus, allowing thatanchor probe to reach into the target nucleic acid for ligation with thethird anchor probe. In further embodiments, one of the anchor probes maybe fully or partially complementary to the adaptor and the second andthird anchor probes will be fully degenerate for hybridization to thetarget nucleic acid. Four or more fully degenerate anchor probes can infurther embodiments be ligated sequentially to the three ligated anchorprobes to achieve extension of reads further into the target nucleicacid sequence. In an exemplary embodiment, a first anchor probecomprising twelve bases complementary to an adaptor may ligate with asecond hexameric anchor probe in which all six bases are degenerate. Athird anchor, also a fully degenerate hexamer, can also ligate to thesecond anchor probe to further extend into the unknown sequence of thetarget nucleic acid. A fourth, fifth, sixth, etc. anchor probe may alsobe added to extend even further into the unknown sequence. In stillfurther embodiments and in accordance with any of the cPAL methodsdescribed herein, one or more of the anchor probes may comprise one ormore labels that serve to “tag” the anchor probe and/or identify theparticular anchor probe hybridized to an adaptor of a DNB.

III.B.1(c) Detecting Fluorescently Labeled Sequencing Probes

As discussed above, sequencing probes used in accordance with thepresent invention may be detectably labeled with a wide variety oflabels. Although the following description is primarily directed toembodiments in which the sequencing probes are labeled withfluorophores, it will be appreciated that similar embodiments utilizingsequencing probes comprising other kinds of labels are encompassed bythe present invention.

Multiple cycles of cPAL (whether single, double, triple, etc.) willidentify multiple bases in the regions of the target nucleic acidadjacent to the adaptors. In brief, the cPAL methods are repeated forinterrogation of multiple bases within a target nucleic acid by cyclinganchor probe hybridization and enzymatic ligation reactions withsequencing probe pools designed to detect nucleotides at varyingpositions removed from the interface between the adaptor and targetnucleic acid. In any given cycle, the sequencing probes used aredesigned such that the identity of one or more of bases at one or morepositions is correlated with the identity of the label attached to thatsequencing probe. Once the ligated sequencing probe (and hence thebase(s) at the interrogation position(s) is detected, the ligatedcomplex is stripped off of the DNB and a new cycle of adaptor andsequencing probe hybridization and ligation is conducted.

In general, four fluorophores are generally used to identify a base atan interrogation position within a sequencing probe, and a single baseis queried per hybridization-ligation-detection cycle. However, as willbe appreciated, embodiments utilizing 8, 16, 20 and 24 fluorophores ormore are also encompassed by the present invention. Increasing thenumber of fluorophores increases the number of bases that can beidentified during any one cycle.

In one exemplary embodiment, a set of 7-mer pools of sequencing probesis employed having the following structures:

3′-F1-NNNNNNAp 3′-F2-NNNNNNGp 3′-F3-NNNNNNCp 3′-F4-NNNNNNTp

The “p” represents a phosphate available for ligation and “N” representsdegenerate bases. F1-F4 represent four different fluorophores—eachfluorophore is thus associated with a particular base. This exemplaryset of probes would allow detection of the base immediately adjacent tothe adaptor upon ligation of the sequencing probe to an anchor probehybridized to the adaptor. To the extent that the ligase used to ligatethe sequencing probe to the anchor probe discriminates forcomplementarity between the base at the interrogation position of theprobe and the base at the detection position of the target nucleic acid,the fluorescent signal that would be detected upon hybridization andligation of the sequencing probe provides the identity of the base atthe detection position of the target nucleic acid.

In some embodiments, a set of sequencing probes will comprise threedifferentially labeled sequencing probes, with a fourth optionalsequencing probe left unlabeled.

After performing a hybridization-ligation-detection cycle, the anchorprobe-sequencing probe ligation products are stripped and a new cycle isbegun. In some embodiments, accurate sequence information can beobtained as far as six bases or more from the ligation point between theanchor and sequencing probes and as far as twelve bases or more from theinterface between the target nucleic acid and the adaptor. The number ofbases that can be identified can be increased using methods describedherein, including the use of anchor probes with degenerate ends that areable to reach further into the target nucleic acid.

Imaging acquisition may be performed using methods known in the art,including the use of commercial imaging packages such as Metamorph(Molecular Devices, Sunnyvale, Calif.). Data extraction may be performedby a series of binaries written in, e.g., C/C++ and base-calling andread-mapping may be performed by a series of Matlab and Peri scripts.

In an exemplary embodiment, DNBs disposed on a surface undergo a cycleof cPAL as described herein in which the sequencing probes utilized arelabeled with four different fluorophores (each corresponding to aparticular base at an interrogation position within the probe). Todetermine the identity of a base of each DNB disposed on the surface,each field of view (“frame”) is imaged with four different wavelengthscorresponding the to the four fluorescently labeled sequencing probes.All images from each cycle are saved in a cycle directory, where thenumber of images is four times the number of frames (when fourfluorophores are used). Cycle image data can then be saved into adirectory structure organized for downstream processing.

In some embodiments, data extraction will rely on two types of imagedata: bright-field images to demarcate the positions of all DNBs on asurface, and sets of fluorescence images acquired during each sequencingcycle. Data extraction software can be used to identify all objects withthe bright-field images and then for each such object, the software canbe used to compute an average fluorescence value for each sequencingcycle. For any given cycle, there are four data points, corresponding tothe four images taken at different wavelengths to query whether thatbase is an A, G, C or T. These raw data points (also referred to hereinas “base calls”) are consolidated, yielding a discontinuous sequencingread for each DNB.

The population of identified bases can then be assembled to providesequence information for the target nucleic acid and/or identify thepresence of particular sequences in the target nucleic acid. In someembodiments, the identified bases are assembled into a complete sequencethrough alignment of overlapping sequences obtained from multiplesequencing cycles performed on multiple DNBs. As used herein, the term“complete sequence” refers to the sequence of partial or whole genomesas well as partial or whole target nucleic acids. In furtherembodiments, assembly methods utilize algorithms that can be used to“piece together” overlapping sequences to provide a complete sequence.In still further embodiments, reference tables are used to assist inassembling the identified sequences into a complete sequence. Areference table may be compiled using existing sequencing data on theorganism of choice. For example human genome data can be accessedthrough the National Center for Biotechnology Information atftp.ncbi.nih.gov/refseq/release, or through the J. Craig VenterInstitute at http://www.jcvi.org/researchhuref/. All or a subset ofhuman genome information can be used to create a reference table forparticular sequencing queries. In addition, specific reference tablescan be constructed from empirical data derived from specificpopulations, including genetic sequence from humans with specificethnicities, geographic heritage, religious or culturally-definedpopulations, as the variation within the human genome may slant thereference data depending upon the origin of the information containedtherein.

In any of the embodiments of the invention discussed herein, apopulation of nucleic acid templates and/or DNBs may comprise a numberof target nucleic acids to substantially cover a whole genome or a wholetarget polynucleotide. As used herein, “substantially covers” means thatthe amount of nucleotides (i.e., target sequences) analyzed contains anequivalent of at least two copies of the target polynucleotide, or inanother aspect, at least ten copies, or in another aspect, at leasttwenty copies, or in another aspect, at least 100 copies. Targetpolynucleotides may include DNA fragments, including genomic DNAfragments and cDNA fragments, and RNA fragments. Guidance for the stepof reconstructing target polynucleotide sequences can be found in thefollowing references, which are incorporated by reference: Lander et al,Genomics, 2: 231-239 (1988); Vingron et al, J. Mol. Biol., 235: 1-12(1994); and like references.

III.B.1(d) Sets of Probes

As will be appreciated, different combinations of sequencing and anchorprobes can be used in accordance with the various cPAL methods describedabove. The following descriptions of sets of probes (also referred toherein as “pools of probes”) of use in the present invention areexemplary embodiments and it will be appreciated that the presentinvention is not limited to these combinations.

In one aspect, sets of probes are designed for identification ofnucleotides at positions at a specific distance from an adaptor. Forexample, certain sets of probes can be used to identify bases up to 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30 and more positions away from the adaptor.As discussed above, anchor probes with degenerate bases at one terminuscan be designed to reach into the target nucleic acid adjacent to anadaptor, allowing sequencing probes to ligate further away from theadaptor and thus provide the identity of a base further away from theadaptor.

In an exemplary embodiment, a set of probes comprises at least twoanchor probes designed to hybridize to adjacent regions of an adaptor.In one embodiment, the first anchor probe is fully complementary to aregion of the adaptor, while the second anchor probe is complementary tothe adjacent region of the adaptor. In some embodiments, the secondanchor probe will comprise one or more degenerate nucleotides thatextend into and hybridize to nucleotides of the target nucleic acidadjacent to the adaptor. In an exemplary embodiment, the second anchorprobe comprises at least 1-10 degenerate bases. In a further exemplaryembodiment, the second anchor probe comprises 2-9, 3-8, 4-7, and 5-6degenerate bases. In a still further exemplary embodiment, the secondanchor probe comprises one or more degenerate bases at one or bothtermini and/or within an interior region of its sequence.

In a further embodiment, a set of probes will also comprise one or moregroups of sequencing probes for base determination in one or moredetection positions with a target nucleic acid. In one embodiment, theset comprises enough different groups of sequencing probes to identifyabout 1 to about 20 positions within a target nucleic acid. In a furtherexemplary embodiment, the set comprises enough groups of sequencingprobes to identify about 2 to about 18, about 3 to about 16, about 4 toabout 14, about 5 to about 12, about 6 to about 10, and about 7 to about8 positions within a target nucleic acid.

In further exemplary embodiments, 10 pools of labeled or tagged probeswill be used in accordance with the invention. In still furtherembodiments, sets of probes will include two or more anchor probes withdifferent sequences. In yet further embodiments, sets of probes willinclude 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more anchorprobes with different sequences.

In a further exemplary embodiment, a set of probes is providedcomprising one or more groups of sequencing probes and three anchorprobes. The first anchor probe is complementary to a first region of anadaptor, the second anchor probe is complementary to a second region ofan adaptor, and the second region and the first region are adjacent toeach other. The third anchor probe comprises three or more degeneratenucleotides and is able to hybridize to nucleotides in the targetnucleic acid adjacent to the adaptor. The third anchor probe may also insome embodiments be complementary to a third region of the adaptor, andthat third region may be adjacent to the second region, such that thesecond anchor probe is flanked by the first and third anchor probes.

In some embodiments, sets of anchor and/or sequencing probes willcomprise variable concentrations of each type of probe, and the variableconcentrations may in part depend on the degenerate bases that may becontained in the anchor probes. For example, probes that will have lowerhybridization stability, such as probes with greater numbers of A'sand/or T's, can be present in higher relative concentrations as a way tooffset their lower stabilities. In further embodiments, thesedifferences in relative concentrations are established by preparingsmaller pools of probes independently and then mixing thoseindependently generated pools of probes in the proper amounts.

III.B.1(e) Two-Phase Sequencing

In one aspect, the present invention provides methods for “two-phase”sequencing, which is also referred to herein as “shotgun sequencing”.Such methods are described in U.S. patent application Ser. No.12/325,922, filed Dec. 1, 2008, which is hereby incorporated byreference in its entirety for all purposes and in particular for allteachings related to two-phase or shotgun sequencing.

Generally, two phase-sequencing methods of use in the present inventioncomprise the following steps: (a) sequencing the target nucleic acid toproduce a primary target nucleic acid sequence that comprises one ormore sequences of interest; (b) synthesizing a plurality oftarget-specific oligonucleotides, wherein each of said plurality oftarget-specific oligonucleotides corresponds to at least one of thesequences of interest; (c) providing a library of fragments of thetarget nucleic acid (or constructs that comprise such fragments and thatmay further comprise, for example, adaptors and other sequences asdescribed herein) that hybridize to the plurality of target-specificoligonucleotides; and (d) sequencing the library of fragments (orconstructs that comprise such fragments) to produce a secondary targetnucleic acid sequence. In order to close gaps due to missing sequence orresolve low confidence base calls in a primary sequence of genomic DNA,such as human genomic DNA, the number of target-specificoligonucleotides that are synthesized for these methods may be fromabout ten thousand to about one million; thus the present inventioncontemplates the use of at least about 10,000 target-specificoligonucleotides, or about 25,000, or about 50,000, or about 100,000, orabout 20,000, or about 50,000, or about 100,000, or about 200,000 ormore.

In saying that the plurality of target-specific oligonucleotides“corresponds to” at least one of the sequences of interest, it is meantthat such target-specific oligonucleotides are designed to hybridize tothe target nucleic acid in proximity to, including but not limited to,adjacent to, the sequence of interest such that there is a highlikelihood that a fragment of the target nucleic acid that hybridizes tosuch an oligonucleotides will include the sequence of interest. Suchtarget-specific oligonucleotides are therefore useful for hybrid capturemethods to produce a library of fragments enriched for such sequences ofinterest, as sequencing primers for sequencing the sequence of interest,as amplification primers for amplifying the sequence of interest, or forother purposes.

In shotgun sequencing and other sequencing methods according to thepresent invention, after assembly of sequencing reads, to the skilledperson it is apparent from the assembled sequence that gaps exist orthat there is low confidence in one or more bases or stretches of basesat a particular site in the sequence. Sequences of interest, which mayinclude such gaps, low confidence sequence, or simply differentsequences at a particular location (i.e., a change of one or morenucleotides in target sequence), can also be identified by comparing theprimary target nucleic acid sequence to a reference sequence.

According to one embodiment of such methods sequencing the targetnucleic acid to produce a primary target nucleic acid sequence comprisescomputerized input of sequence readings and computerized assembly of thesequence readings to produce the primary target nucleic acid sequence.In addition, design of the target-specific oligonucleotides can becomputerized, and such computerized synthesis of the target-specificoligonucleotides can be integrated with the computerized input andassembly of the sequence readings and design of the target-specificoligonucleotides. This is especially helpful since the number oftarget-specific oligonucleotides to be synthesized can be in the tens ofthousands or hundreds of thousands for genomes of higher organisms suchas humans, for example. Thus the invention provides automatedintegration of the process of creating the oligonucleotide pool from thedetermined sequences and the regions identified for further processing.In some embodiments, a computer-driven program uses the identifiedregions and determined sequence near or adjacent to such identifiedregions to design oligonucleotides to isolate and/or create newfragments that cover these regions. The oligonucleotides can then beused as described herein to isolate fragments, either from the firstsequencing library, from a precursor of the first sequencing library,from a different sequencing library created from the same target nucleicacid, directly from target nucleic acids, and the like. In furtherembodiments, this automated integration of identifying regions forfurther analysis and isolating/creating the second library defines thesequence of the oligonucleotides within the oligonucleotide pool anddirects synthesis of these oligonucleotides.

In some embodiments of the two phase sequencing methods of theinvention, a releasing process is performed after the hybrid captureprocess, and in other aspects of the technology, an amplificationprocess is performed before the second sequencing process.

In still further embodiments, some or all regions are identified in theidentifying step by comparison of determined sequences with a referencesequence. In some aspects, the second shotgun sequencing library isisolated using a pool of oligonucleotides comprising oligonucleotidesbased on a reference sequence. Also, in some aspects, the pool ofoligonucleotides comprises at least 1000 oligonucleotides of differentsequence, in other aspects, the pool of oligonucleotides comprises atleast 10,000, 25,000, 50,000, 75,000, or 100,000 or moreoligonucleotides of different sequence

In some aspects of the invention, one or more of the sequencingprocesses used in this two-phase sequencing method is performed bysequencing-by-ligation, and in other aspects, one or more of thesequencing processes is performed by sequencing-by-hybridization orsequencing-by-synthesis.

In certain aspects of the invention, between about 1 to about 30% of thecomplex target nucleic acid is identified as having to be re-sequencedin Phase II of the methods, and in other aspects, between about 1 toabout 10% of the complex target nucleic acid is identified as having tobe re-sequenced in Phase II of the methods. In some aspects, coveragefor the identified percentage of complex target nucleic acid is betweenabout 25× to about 100×.

In further aspects, 1 to about 10 target-specific selectionoligonucleotides are defined and synthesized for each target nucleicacid region that is re-sequenced in Phase II of the methods; in otheraspects, about 3 to about 6 target-specific selection oligonucleotidesare defined for each target nucleic acid region that is re-sequenced inPhase II of the methods.

In still further aspects of the technology, the target-specificselection oligonucleotides are identified and synthesized by anautomated process, wherein the process that identifies regions of thecomplex nucleic acid missing nucleic acid sequence or having lowconfidence nucleic acid sequence and defines sequences for thetarget-specific selection oligonucleotides communicates witholigonucleotide synthesis software and hardware to synthesize thetarget-specific selection oligonucleotides. In other aspects of thetechnology, the target-specific selection oligonucleotides are betweenabout 20 and about 30 bases in length, and in some aspects areunmodified.

Not all regions identified for further analysis may actually exist inthe complex target nucleic acid. One reason for predicted lack ofcoverage in a region may be that a region expected to be in the complextarget nucleic acid may actually not be present (e.g., a region may bedeleted or re-arranged in the target nucleic acid), and thus not alloligonucleotides produced from the pool may isolate a fragment forinclusion in the second shotgun sequencing library. In some embodiments,at least one oligonucleotide will be designed and created for eachregion identified for further analysis. In further embodiments, anaverage of three or more oligonucleotides will be provided for eachregion identified for further analysis. It is a feature of the inventionthat the pool of oligonucleotides can be used directly to create thesecond shotgun sequencing library by polymerase extension of theoligonucleotides using templates derived from a target nucleic acid. Itis another feature of the invention that the pool of oligonucleotidescan be used directly to create amplicons via circle dependentreplication using the oligonucleotide pools and circle dependentreplication. It is another feature of the invention that the methodswill provide sequencing information to identify absent regions ofinterest, e.g. predicted regions that were identified for analysis butwhich do not exist, e.g., due to a deletion or rearrangement.

The above described embodiments of the two-phase sequencing method canbe used in combination with any of the nucleic acid constructs andsequencing methods described herein and known in the art.

III.B.1(t) SNP Detection

Methods and compositions discussed above can in further embodiments beused to detect specific sequences in nucleic acid constructs such asDNBs. In particular, cPAL methods utilizing sequencing and anchor probescan be used to detect polymorphisms or sequences associated with agenetic mutation, including single nucleotide polymorphisms (SNPs). Forexample, to detect the presence of a SNP, two sets of differentiallylabeled sequencing probes can be used, such that detection of one probeover the other indicates whether a polymorphism present in the sample.Such sequencing probes can be used in conjunction with anchor probes inmethods similar to the cPAL methods described above to further improvethe specificity and efficiency of detection of the SNP.

IV. Arrays

In one aspect, nucleic acids, including LFR aliquot fragments and DNBs,are disposed on a surface to form a random array of single molecules.Nucleic acids can be fixed to surface by a variety of techniques,including covalent attachment and non-covalent attachment. Non-covalentattachment includes hydrogen bonding, van der Waals forces,electrostatic attraction and the like.

Methods for forming arrays of the invention are described in PublishedPatent Application Nos. WO2007120208, WO2006073504, WO2007133831, andUS2007099208, and U.S. Patent Application Nos. 60/992,485; 61/026,337;61/035,914; 61/061,134; 61/116,193; 61/102,586; Ser. Nos. 12/265,593;12/266,385; 11/938,096; 11/981,804; Nos. 11/981,797; 11/981,793;11/981,767; 11/981,761; 11/981,730; 11/981,685; 11/981,661; 11/981,607;11/981,605; 11/927,388; 11/927,356; 11/679,124; 11/541,225; 10/547,214;11/451,692; and 11/451,691, all of which are incorporated herein byreference in their entirety for all purposes and in particular for allteachings related to forming arrays.

In some embodiments, patterned substrates are formed by growing a layerof silicon dioxide on the surface of a standard silicon wafer. A layerof metal, such as titanium, is deposited over silicon dioxide, and thetitanium layer is patterned with fiducial markings with conventionalphotolithography and dry etching techniques. A layer ofhexamethyldisilazane (HMDS) (Gelest Inc., Morrisville, Pa.) can then beadded to the substrate surface by vapor deposition, and a deep-UV,positive-tone photoresist material is coated to the surface bycentrifugal force. The photoresist surface can then be exposed with thearray pattern with a 248 nm lithography tool, and the resist developedto produce arrays having discrete regions of exposed HMDS. The HMDSlayer in the holes can be removed, in some embodiments with aplasma-etch process, and functional moieties can be vapor-deposited inthe holes to provide attachment sites for nucleic acids. In certainembodiments, these functional moieties are aminosilane moieties, whichprovide a positive charge that can be used to non-covalently immobilizenucleic acids through electrostatic attraction. Surfaces can in someembodiments be further coated with a layer of photoresist afterdeposition of aminosilane moieties and cut into substrates of apredetermined size. For example, in some embodiments substrates of 75mm×25 mm area are of use in aspects of the present invention. In furtherembodiments, photoresist material can be stripped from individualsubstrates using methods known in the art, including ultrasonication. Instill further embodiments, regions between the discrete aminosilanefeatures are inert to prevent nucleic acid binding to the spaces betweendiscrete regions. For example, the aminosilane features patterned ontothe substrate in accordance with the embodiments described herein serveas nucleic acid binding sites, whereas the remaining HMDS inhibitsnucleic acid binding between features. In yet further embodiments, amixture of polystyrene beads and polyurethane glue is applied in aseries of parallel lines to each diced substrate, and a coverslippressed into the flue lines to form a six-lane gravity/capillary-drivenflow slide. In certain embodiments, the polystyrene beads are 50 μmbeads. Nucleic acids can be loaded into flow slide lanes by pipettingnucleic acids onto the slide. In certain embodiments, a larger quantityof nucleic acids is applied to the slide than the number of bindingsites present on the slide. In further exemplary embodiments, 2-20 foldmore nucleic acid single molecules than binding sites are applied to theslide. In still further embodiments, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, and 20 fold more nucleic acid singlemolecules than binding sites are applied to the slide.

As will be appreciated, a wide range of densities of nucleic acids ofthe invention can be placed on a surface comprising discrete regions toform an array. Nucleic acids are generally immobilized to the discreteregions by a variety of methods known in the art and described infurther detail below. In specific embodiments, nucleic acids areimmobilized to discrete regions on an array through non-covalentelectrostatic interactions.

In preferred embodiments, at least a majority of the discrete regionscomprises a single molecule attached thereto, and the discrete regionsand/or the single molecules are distributed such that at least amajority of the single molecules immobilized to the discrete regions areoptically resolvable. In further embodiments, at least 50%-100% of thediscrete regions have a single molecule attached thereto. In stillfurther embodiments, at least 55%-95%, 60%-90%, 65%-85%, and 70%-80% ofthe discrete regions on an array have a single molecule attachedthereto. In yet further embodiments, at least 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 96%, 97%, 98%, and 99% of discrete regions on an arrayhave a single molecule attached thereto.

In further embodiments, at least at least 50%-100% of the singlemolecules on a random array of the invention are optically resolvable.In still further embodiments, at least 55%-95%, 60%-90%, 65%-85%, and70%-80% of the single molecules on a random array of the invention areoptically resolvable. In yet further embodiments, at least 60%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, and 99% of the singlemolecules on a random array of the invention are optically resolvable.

In some embodiments, the area of discrete regions is less than 1 μm²;and in some embodiments, the area of discrete regions is in the range offrom 0.04 μm² to 1 μm²; and in some embodiments, the area of discreteregions is in the range of from 0.2 μm² to 1 μm². In still furtherembodiments, the area of the discrete regions is about 0.1, 0.2, 0.3,0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5 μm². In embodiments inwhich discrete regions are approximately circular or square in shape sothat their sizes can be indicated by a single linear dimension, the sizeof such regions are in the range of from 125 nm to 250 nm, or in therange of from 200 nm to 500 nm. In some embodiments, center-to-centerdistances of nearest neighbors of discrete regions are in the range offrom 0.25 μm to 20 μm; and in some embodiments, such distances are inthe range of from 1 μm to 10 μm, or in the range from 50 to 1000 nm. Instill further embodiments, center-to-center distances of nearestneighbors of discrete regions are in the range of from about 100-900,200-800, 300-700, 400-500 nm. In yet further embodiments,center-to-center distances of nearest neighbors of discrete regions arein the range of from about 650-750, 660-740, 650-730, 660-720, 670-710,680-700, 700-710 nm. In certain embodiments, center-to-center distancesof nearest neighbors of discrete regions are 707 nm. Generally, discreteregions are designed such that a majority of the discrete regions on asurface are optically resolvable. In some embodiments, regions may bearranged on a surface in virtually any pattern in which regions havedefined locations. As discussed in further detail above, in certainembodiments, a single nucleic acid is attached to each of at least amajority of discrete regions on a surface.

In some embodiments, an array of the invention comprises 1, 2, 3, 4, 5,6, 7, 8, 9, or 10 single molecules per square micron.

In some embodiments, arrays of nucleic acids are provided in densitiesof at least 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 million molecules persquare millimeter.

In some embodiments, nucleic acids are randomly disposed on substratesdescribed herein and known in the art at a density such that eachdiscrete region comprises a single nucleic acid molecule immobilizedthereto. In further embodiments, nucleic acids are disposed onsubstrates at a density of 100, 200, 500, 750, 1000, 2000, 3000, 4000,5000, 10,000, 50,000, 100,000, 250,000, 500,000, 750,000, 1,000,000molecules per square micron.

In some embodiments, a surface may have reactive functionalities thatreact with complementary functionalities on the polynucleotide moleculesto form a covalent linkage, e.g., by way of the same techniques used toattach cDNAs to microarrays, e.g., Smirnov et al (2004), Genes,Chromosomes & Cancer, 40: 72-77; Beaucage (2001), Current MedicinalChemistry, 8: 1213-1244, which are incorporated herein by reference.Nucleic acids may also be efficiently attached to hydrophobic surfaces,such as a clean glass surface that has a low concentration of variousreactive functionalities, such as —OH groups. Attachment throughcovalent bonds formed between the polynucleotide molecules and reactivefunctionalities on the surface is also referred to herein as “chemicalattachment”.

In one aspect, nucleic acids on a surface are confined to an area of adiscrete region. Discrete regions may be incorporated into a surfaceusing methods known in the art and described further below. As will beappreciated, nucleic acids of the invention can be immobilized todiscrete regions through non-specific interactions, or throughnon-covalent interactions such as hydrogen bonding, van der Waalsforces, electrostatic attraction and the like. Nucleic acids may also beattached to discrete regions through the use of capture probes orthrough covalent interaction with reactive functionalities, as is knownin the art and described in further detail herein. As will beappreciated, attachment may also include wash steps of varyingstringencies to remove incompletely attached single molecules or otherreagents present from earlier preparation steps whose presence isundesirable or that are nonspecifically bound to surface.

The discrete regions may have defined locations in a regular array,which may correspond to a rectilinear pattern, hexagonal pattern, or thelike. A regular array of such regions is advantageous for detection anddata analysis of signals collected from the arrays during an analysis.Also, first- and/or second-stage amplicons confined to the restrictedarea of a discrete region provide a more concentrated or intense signal,particularly when fluorescent probes are used in analytical operations,thereby providing higher signal-to-noise values. In some embodiments,nucleic acids are randomly distributed on the discrete regions so that agiven region is equally likely to receive any of the different singlemolecules. In other words, the resulting arrays are not spatiallyaddressable immediately upon fabrication, but may be made so by carryingout an identification, sequencing and/or decoding operation. As such,the identities of the polynucleotide molecules of the invention disposedon a surface are discernable, but not initially known upon theirdisposition on the surface. In some embodiments, the area of discrete isselected, along with attachment chemistries, macromolecular structuresemployed, and the like, to correspond to the size of single molecules ofthe invention so that when single molecules are applied to surfacesubstantially every region is occupied by no more than one singlemolecule. In some embodiments, nucleic acids are disposed on a surfacecomprising discrete regions in a patterned manner, such that specificnucleic acids (identified, in an exemplary embodiment, by tag adaptorsor other labels) are disposed on specific discrete regions or groups ofdiscrete regions.

In further embodiments, molecules are directed to the discrete regionsof a surface, because the areas between the discrete regions, referredto herein as “inter-regional areas,” are inert, in the sense thatconcatemers, or other macromolecular structures, do not bind to suchregions. In some embodiments, such inter-regional areas may be treatedwith blocking agents, e.g., DNAs unrelated to concatemer DNA, otherpolymers, and the like.

A wide variety of supports may be used with the compositions and methodsof the invention to form random arrays. In one aspect, supports arerigid solids that have a surface, preferably a substantially planarsurface so that single molecules to be interrogated are in the sameplane. The latter feature permits efficient signal collection bydetection optics, for example. In another aspect, the support comprisesbeads, wherein the surface of the beads comprise reactivefunctionalities or capture probes that can be used to immobilizepolynucleotide molecules.

In still another aspect, solid supports of the invention are nonporous,particularly when random arrays of single molecules are analyzed byhybridization reactions requiring small volumes. Suitable solid supportmaterials include materials such as glass, polyacrylamide-coated glass,ceramics, silica, silicon, quartz, various plastics, and the like. Inone aspect, the area of a planar surface may be in the range of from 0.5to 4 cm². In one aspect, the solid support is glass or quartz, such as amicroscope slide, having a surface that is uniformly silanized. This maybe accomplished using conventional protocols, e.g., acid treatmentfollowed by immersion in a solution of 3-glycidoxypropyltrimethoxysilane, N,N-diisopropylethylamine, and anhydrous xylene(8:1:24 v/v) at 80° C., which forms an epoxysilanized surface. e.g.,Beattie et al (1995), Molecular Biotechnology, 4: 213. Such a surface isreadily treated to permit end-attachment of capture oligonucleotides,e.g., by providing capture oligonucleotides with a 3′ or 5′ triethyleneglycol phosphoryl spacer (see Beattie et al, cited above) prior toapplication to the surface. Further embodiments for functionalizing andfurther preparing surfaces for use in the present invention aredescribed for example in U.S. Patent Application Ser. Nos. 60/992,485;61/026,337; 61/035,914; 61/061,134; 61/116,193; 61/102,586; 12/265,593;12/266,385; 11/938,096; 11/981,804; Nos. 11/981,797; 11/981,793;11/981,767; 11/981,761; 11/981,730; 11/981,685; 11/981,661; 11/981,607;11/981,605; 11/927,388; 11/927,356; 11/679,124; 11/541,225; 10/547,214;11/451,692; and 11/451,691, each of which is herein incorporated byreference in its entirety for all purposes and in particular for allteachings related to preparing surfaces for forming arrays and for allteachings related to forming arrays, particularly arrays of nucleicacids.

In embodiments of the invention in which patterns of discrete regionsare required, photolithography, electron beam lithography, nano imprintlithography, and nano printing may be used to generate such patterns ona wide variety of surfaces, e.g., Pirrung et al, U.S. Pat. No.5,143,854; Fodor et al, U.S. Pat. No. 5,774,305; Guo, (2004) Journal ofPhysics D: Applied Physics, 37: R123-141; which are incorporated hereinby reference.

In one aspect, surfaces containing a plurality of discrete regions arefabricated by photolithography. A commercially available, opticallyflat, quartz substrate is spin coated with a 100-500 nm thick layer ofphoto-resist. The photo-resist is then baked on to the quartz substrate.An image of a reticle with a pattern of regions to be activated isprojected onto the surface of the photo-resist, using a stepper. Afterexposure, the photo-resist is developed, removing the areas of theprojected pattern which were exposed to the UV source. This isaccomplished by plasma etching, a dry developing technique capable ofproducing very fine detail. The substrate is then baked to strengthenthe remaining photo-resist. After baking, the quartz wafer is ready forfunctionalization. The wafer is then subjected to vapor-deposition of3-aminopropyldimethylethoxysilane. The density of the aminofunctionalized monomer can be tightly controlled by varying theconcentration of the monomer and the time of exposure of the substrate.Only areas of quartz exposed by the plasma etching process may reactwith and capture the monomer. The substrate is then baked again to curethe monolayer of amino-functionalized monomer to the exposed quartz.After baking, the remaining photo-resist may be removed using acetone.Because of the difference in attachment chemistry between the resist andsilane, aminosilane-functionalized areas on the substrate may remainintact through the acetone rinse. These areas can be furtherfunctionalized by reacting them with p-phenylenediisothiocyanate in asolution of pyridine and N—N-dimethlyformamide. The substrate is thencapable of reacting with amine-modified oligonucleotides. Alternatively,oligonucleotides can be prepared with a 5′-carboxy-modifier-c10 linker(Glen Research). This technique allows the oligonucleotide to beattached directly to the amine modified support, thereby avoidingadditional functionalization steps.

In another aspect, surfaces containing a plurality of discrete regionsare fabricated by nano-imprint lithography (NIL). For DNA arrayproduction, a quartz substrate is spin coated with a layer of resist,commonly called the transfer layer. A second type of resist is thenapplied over the transfer layer, commonly called the imprint layer. Themaster imprint tool then makes an impression on the imprint layer. Theoverall thickness of the imprint layer is then reduced by plasma etchinguntil the low areas of the imprint reach the transfer layer. Because thetransfer layer is harder to remove than the imprint layer, it remainslargely untouched. The imprint and transfer layers are then hardened byheating. The substrate is then put into a plasma etcher until the lowareas of the imprint reach the quartz. The substrate is then derivatizedby vapor deposition as described above.

In another aspect, surfaces containing a plurality of discrete regionsare fabricated by nano printing. This process uses photo, imprint, ore-beam lithography to create a master mold, which is a negative image ofthe features required on the print head. Print heads are usually made ofa soft, flexible polymer such as polydimethylsiloxane (PDMS). Thismaterial, or layers of materials having different properties, are spincoated onto a quartz substrate. The mold is then used to emboss thefeatures onto the top layer of resist material under controlledtemperature and pressure conditions. The print head is then subjected toa plasma based etching process to improve the aspect ratio of the printhead, and eliminate distortion of the print head due to relaxation overtime of the embossed material. Random array substrates are manufacturedusing nano-printing by depositing a pattern of amine modifiedoligonucleotides onto a homogenously derivatized surface. Theseoligonucleotides would serve as capture probes for nucleic acids. Onepotential advantage to nano-printing is the ability to print interleavedpatterns of different capture probes onto the random array support. Thiswould be accomplished by successive printing with multiple print heads,each head having a differing pattern, and all patterns fitting togetherto form the final structured support pattern. Such methods allow forsome positional encoding of DNA elements within the random array. Forexample, control concatemers containing a specific sequence can be boundat regular intervals throughout a random array.

In still another aspect, a high density array of capture oligonucleotidespots of sub micron size is prepared using a printing head orimprint-master prepared from a bundle, or bundle of bundles, of about10,000 to 100 million optical fibers with a core and cladding material.By pulling and fusing fibers a unique material is produced that hasabout 50-1000 nm cores separated by a similar or 2-5 fold smaller orlarger size cladding material. By differential etching (dissolving) ofcladding material a nano-printing head is obtained having a very largenumber of nano-sized posts. This printing head may be used fordepositing oligonucleotides or other biological (proteins,oligopeptides, DNA, aptamers) or chemical compounds such as silane withvarious active groups. In one embodiment the glass fiber tool is used asa patterned support to deposit oligonucleotides or other biological orchemical compounds. In this case only posts created by etching may becontacted with material to be deposited. Also, a flat cut of the fusedfiber bundle may be used to guide light through cores and allowlight-induced chemistry to occur only at the tip surface of the cores,thus eliminating the need for etching. In both cases, the same supportmay then be used as a light guiding/collection device for imagingfluorescence labels used to tag oligonucleotides or other reactants.This device provides a large field of view with a large numericalaperture (potentially >1). Stamping or printing tools that performactive material or oligonucleotide deposition may be used to print 2 to100 different oligonucleotides in an interleaved pattern. This processrequires precise positioning of the print head to about 50-500 nm. Thistype of oligonucleotide array may be used for attaching 2 to 100different DNA populations such as different source DNA. They also may beused for parallel reading from sub-light resolution spots by using DNAspecific anchors or tags. Information can be accessed by DNA specifictags, e.g., 16 specific anchors for 16 DNAs and read 2 bases by acombination of 5-6 colors and using 16 ligation cycles or one ligationcycle and 16 decoding cycles. This way of making arrays is efficient iflimited information (e.g., a small number of cycles) is required perfragment, thus providing more information per cycle or more cycles persurface.

In one aspect, multiple arrays of the invention may be placed on asingle surface. For example, patterned array substrates may be producedto match the standard 96 or 384 well plate format. A production formatcan be an 8×12 pattern of 6 mm×6 mm arrays at 9 mm pitch or 16×24 of3.33 mm×3.33 mm array at 4.5 mm pitch, on a single piece of glass orplastic and other optically compatible material. In one example each 6mm×6 mm array consists of 36 million 250-500 nm square regions at 1micrometer pitch. Hydrophobic or other surface or physical barriers maybe used to prevent mixing different reactions between unit arrays.

Other methods of forming arrays of molecules are known in the art andare applicable to forming arrays.

V. Exemplary Embodiments

The following provide certain exemplary embodiments of the invention. Itwill be appreciated that these embodiments may be altered or expandedusing methods well within the skills of one in the art. Since manyaspects can be made without departing from the spirit and scope of thepresently described technology, the appropriate scope resides in theclaims hereinafter appended. Other aspects are therefore contemplated.Furthermore, it should be understood that any operations may beperformed in any order, unless explicitly claimed otherwise or aspecific order is inherently necessitated by the claim language.

In an exemplary embodiment, the present invention provides a method offragmenting a double-stranded target nucleic acid. This method includes(a) providing genomic DNA; (b) dividing DNA into a number of separatealiquots; (c) amplifying the DNA in the separate aliquots in thepresence of a population of dNTPs that includes dNTP analogs, such thata number of nucleotides in the DNA are replaced by dNTP analogs; (d)removing the dNTP analogs to form gapped DNA; (e) treating the gappedDNA to translate the gaps until gaps on opposite strands converge,thereby creating blunt-ended DNA fragments. In a further embodiment,substantially every fragment in a separate mixture is non-overlappingwith every other fragment of the same aliquot.

In a further embodiment and in accordance with the above, the dNTPanalogs are selected from a group that includes inosine, uracil and5-methyl cytosine.

In a still further embodiment and in accordance with any of the above,the dNTP analogs include both deoxy-uracil and 5-methyl cytosine.

In a further embodiment and in accordance with any of the above, methodsof the invention include a further step of obtaining a number ofsequence reads from fragments of each separate mixture.

In a further embodiment and in accordance with any of the above, priorto obtaining sequence reads, the fragments are used to generate DNAnanoballs.

In a further embodiment and in accordance with any of the above, theseparate mixtures comprise on average less than about 0.1%, 0.3%, 1%, or3% of the genome.

In a further embodiment and in accordance with any of the above, thepresent invention provides a method for fragmenting nucleic acids thatincludes the steps of: (a) providing at least two genome-equivalents ofDNA for at least one genome; (b) dividing the DNA into a first tier ofseparate mixtures; (c) amplifying the DNA in the separate mixtures,wherein the amplifying is conducted with a population of dNTPs thatcomprises a predetermined ratio of dUTP to dTTP, such that a number ofthymines in said DNA are replaced by uracils, and a predetermined ratioof 5-methyl dCTP to dCTP, such that a number of cytosines are replacedby 5-methyl cytosines; (d) removing the uracils and the 5-methylcytosines to form gapped DNA; (e) treating the gapped DNA to translatesaid gaps until gaps on opposite strands converge, thereby creatingblunt-ended DNA fragments, where the blunt-ended fragments have less GCbias and less coverage bias as compared to fragments generated in theabsence of 5-methyl cytosine.

In a further embodiment and in accordance with any of the above,sequence reads from fragments of each separate mixture of the first tierare obtained.

In a further embodiment and in accordance with any of the above, theseparate mixtures of fragments are separated further into a second tierof separate mixtures. In a still further embodiment, sequence reads areobtained from fragments of each separate mixture in the second tier.

In a further embodiment and in accordance with any of the above, theseparate mixtures in either a first, second or greater tier ofaliquoting and/or fragmenting have a volume of less than 1 μl, 100 nl,10 nl, 1 nl or 100 pl.

In a further embodiment and in accordance with any of the above,amplification is conducted in the presence of a member selected fromglycogen, DMSO, ET SSB, betaine, and any combination thereof.

In a further embodiment and in accordance with any of the above, afterone or more rounds of fragmenting, the fragments have lengths of about100 kb to about 1 mb.

In a further embodiment and in accordance with any of the above, thepresent invention provides a method of fragmenting a double-strandedtarget nucleic acid that includes the steps of: (a) providing genomicDNA; (b) dividing the DNA into separate aliquots; (c) amplifying the DNAin the separate aliquots to form a plurality of amplicons, where theamplifying is conducted with a population of dNTPs that comprises dNTPanalogs, such that a number of nucleotides in the amplicons are replacedby the dNTP analogs; and wherein the amplifying is conducted in thepresence of an additive selected from glycogen, DMSO, ET SSB, betaine,and any combination thereof; (c) removing the dNTP analogs from theamplicons to form gapped DNA; (d) treating the gapped DNA to translatesaid gaps until gaps on opposite strands converge, thereby creatingblunt-ended DNA fragments, wherein the blunt-ended fragments have lessGC bias as compared to fragments generated in the absence of theadditive.

In a further embodiment and in accordance with any of the above, anumber of sequence reads are obtained from fragments of each separatemixture.

In a further embodiment and in accordance with any of the above, thefragments of each separate mixture are amplified a second time before orafter the step of obtaining sequence reads.

In a further embodiment and in accordance with any of the above, thedNTP analogs are selected from a group that includes inosine, uracil and5-methyl cytosine.

In a further embodiment and in accordance with any of the above, thedNTP analogs include both deoxy-uracil and 5-methyl cytosine.

In a further embodiment and in accordance with any of the above, thefragments have lengths of from about 10,000 to about 200,000 bp.

In a further embodiment and in accordance with any of the above, thefragments have lengths of about 100,000 bp.

In a further embodiment and in accordance with any of the above, thepresent invention provides a method of obtaining sequence informationfrom a genome that includes the steps: (a) providing a population offirst fragments of said genome; (b) preparing emulsion droplets of thefirst fragments, such that each emulsion droplet comprises a subset ofthe population of first fragments; (c) obtaining a population of secondfragments within each emulsion droplet, such that the second fragmentsare shorter than the first fragments from which they are derived; (d)combining the emulsion droplets of the second fragments with emulsiondroplets of adaptor tags; (e) ligating the second fragments with theadaptor tags to form tagged fragments; (f) combining the taggedfragments into a single mixture; (g) obtaining sequence reads from thetagged fragments, where the sequence reads include sequence informationfrom the adaptor tags and the fragments to identify fragments from thesame emulsion droplet, thereby providing sequence information for thegenome.

In a further embodiment and in accordance with any of the above, theemulsion droplets of the adaptors include at least two sets of differenttag components such that fragments in at least some of the emulsiondroplets are tagged with different combinations of the tag components inthe ligating step (f).

In a further embodiment and in accordance with any of the above, atleast 1000 different emulsion droplets include fragments tagged withdifferent combinations of the tag components.

In a further embodiment and in accordance with any of the above, atleast 10,000; 30,000; or 100,000 different emulsion droplets includefragments tagged with different combinations of tag components.

In a further embodiment and in accordance with any of the above, the tagcomponents are from a set of over 1000 distinct barcodes prepared as apopulation of liquid drops in oil.

In a further embodiment and in accordance with any of the above, theemulsion droplets of the first fragments comprise only 1-5 firstfragments in each droplet.

In a further embodiment and in accordance with any of the above, theemulsion droplets of the fragments or the emulsion droplets of theadaptors further comprise ligase and/or other reagents needed for aligation reaction.

EXAMPLES Example 1 Overview of LFR Technology

As illustrated in FIG. 30(A), genomic DNA is released from 1-100 cellsand maintained as long fragments from 100 kb to 1 mb in size. DNA isreplicated if a few cells are used. Blue represents the maternal and redthe paternal fragment of a selected loci. In FIG. 30 (B), the longgenomic DNA is split into 1000 to 100,000 aliquots (e.g., a 1536- or6144-well plate or >10,000 nanoliter drops such as in RainDance orAdvanced Liquid Logic systems) containing 1% or as low as 0.01% of ahaploid genome (1-1,000 fragments per aliquot). In FIG. 30 (C), DNA isamplified (not necessary for some platforms) by phi29 polymerase(resulting DNA can be shorter than original), enzymatically fragmentedto 100-10,000 bp (standard is 500 bp), and uniquely bar-coded in eachaliquot via combinatorial DNA adapter ligation with unique 6- to 12-mersequence. In FIG. 30 (D), aliquots are pooled into a single reaction. InFIG. 30 (E) barcoded DNA is incorporated into standard librarypreparation and DNA and barcodes are sequenced. Minimal mapping oftagged-reads to the entire reference determines which regions of thegenome to use as a short composite reference for fast read assembly inindividual aliquots. Computational cost of read mapping is thus reduced100 fold. In FIG. 30 (F), tagged-reads are used to independentlyassemble maternal and paternal 100+ kb fragments of genome. Overlapping100+ kb fragments (e.g., from aliquots 3 and 77) are recognized byshared SNP alleles and used to independently assemble sequences ofmaternal and paternal chromosomes. Ten cells provide fragments thatoverlap over 90+ kb, on average, with ˜60 heterozygote variants thatensure correct parental mapping.

Example 2 Miniaturization of LFR

As shown in FIG. 28(A), 96-384 uniquely barcoded half adapters from SetA and Set B are combined in a pair wise fashion into about 10K-150Kdistinct individual combinatorial adapter oil-water droplets. In FIG.28(B), up to 10 billion combinatorial adapter droplets in 10 ml areformed (in a few days) and stored. This amount is sufficient to processover 1000 human samples. In FIG. 28(C), combinatorial adapter dropletsfrom (B) are fed into a microfluidic device and merged one-to-one withdrops of amplified fragmented DNA generated from sub-genome aliquotsof >100 kb fragments, FIG. 28(D), fragmented DNA in 10,000 or moreemulsion droplets is ligated to unique combinatorial adapters. In FIG.28(E) is shown a magnified view of a combinatorial adapter. Yellowrepresents 4-6 bps components of barcode sequence; blue and redrepresent Set A and Set B common adapter sequence, respectively. Set Aand B adapters have 2-4 bps of complementary sequence for improveddirectional ligation; B is blocked (“|”) from ligating to genomic DNA(black). In FIG. 28(F), after adapter ligation individual emulsiondroplets are broken and DNA fragments are pooled for entry into standardlibrary preparation.

Example 3 Using LFR Data to Define Haplotypes

An example of a consensuses chromosomal sequence with 4 heterozygotesites at variable distances of 3 to 35 kb is depicted in FIG. 29.Starting from the left, the percent of shared aliquots (PSA) iscalculated for each pair of neighboring alleles. The numbers for 4possible pairs are written in the following order: top-top, top-bottom,bottom-top, and bottom-bottom (e.g., numbers 7, 87, 83, and 0) for the 7kb segment correspond to A-C, A-T, G-C and G-T pairs, respectively. If20 cells are used an allele can be found in 20 or less aliquots. For A-Cand A-T pairs only A aliquots lacking G are used. For G-C and G-T pairsonly G aliquots lacking A are used. For A-T pair, if A without G ispresent in 15 aliquots, T is present in 17 aliquots and A and T arepresent together in 13 aliquots, the PSA is 13/15=87%.

Example 4 φ29 Mediated Overlapping Genomic Fragments

Long fragment genomic DNA can treated with a low concentration of aninfrequent nicking enzyme. φ29 polymerase molecules simultaneouslyextend DNA from the nicks displacing proceeding DNA strands. Completeextension results in long overlapping fragments without loss of DNA atfragment ends.

Example 5 Sequencing Cancer Samples

Four cancer samples with matched normal cells are sequenced using LFRtechniques discussed herein. Emulsion technology or libraries in3072-6144 aliquots are used. Complete methylome data is also generatedat the same time. Depending on the cost reduction achieved more than 120Gb of data may be obtained per genome. The results from the experimentsdemonstrate the completeness and quality of sequence, and the nature ofgenetic and epigenetic changes in the analyzed cancer tissues.

Example 6 MDA Reaction for Inserting Uracils for CoRE

An aliquot of DNA was diluted to 1 ng/μL. Excessive pipetting is avoidedto help retain long fragment lengths. No vortexing is conducted of themixtures at any point of preparing the reaction.

A ⅕ dilution of denaturation buffer was made from concentrated frozenstock. The denaturation buffer contained:

  1 mL 1M KOH   50 uL 500 mM EDTA 1.45 mL dH2O 2.5 mL of 400 mM KOH, 10mM EDTA

5 ng (5 μL) of the 1 ng/μL DNA was diluted in 45 μL of 1× glycogenwater.

The DNA was denatured by adding 50 μL of a ⅕ dilution of denaturationbuffer (the total current volume is 100 μL). The final concentration ofthis mix will be 50 pg/μL.

The mixture was incubated for 5 minutes.

DNA needed for the number of wells/aliquots is removed to create aconcentration of 0.025 genome equivalents per μL (i.e., 0.0825 pg/μL)and placed in a tube, well or other method of aliquot storage. Inembodiments using wells, the amount is determined using the followingcalculation: DNA (μL)−[0.0825 pg/μL)×(2 μL)×(# aliquots/wells)]/50pg/μL.

An appropriate amount of 1 mM 9-mer primer (0.03 μL per well) was addedto the denatured DNA from the above step and incubated for 1 minute. Theappropriate amount was calculated from the number of aliquots that wouldbe used. For example, for 405 wells, this would be equal to 0.03 μL×(#aliquots)=12.2 μL.

The reaction was neutralized with an appropriate amount of a 1/45dilution of neutralization buffer (used ½ the volume of denatured DNAfrom the removal step described above). The neutralization buffercontained the following:

4 mL 1M HCl 6 mL 1M Tris-HCl buffer, pH 7.5 10 mL  final pH of thesolution is 0.6

The reaction was then diluted to 0.025 genome equivalents in distilledwater with 1× glycogen. For embodiments using multi-well formats, thecalculation was [(# of wells×2 μL)−(μL of denatured DNA+μL of bufferN+μL of 9mer]—for a 405 well plate, this would be(405×2)−(1.33+0.67+12.2)=796 μL. 2 μL of the mixture was then added toeach well.

A 4.0% dUTP-MDA mix was created according to the protocol set out below(an example for 405 wells is shown):

1X 405X 3X master mix 0.9625 ul 389.8 ul Φ29 (Enzymatics 10U/ul) 0.0375ul  15.2 ul  1.0 ul   405 ul

The 3× master mix contained the following:

1 well 10000 wells 10X Φ buffer .3 μL 3 ml 25 mM dNTPs (USB) .03 μL 300μL 0.4% PO34 .075 μL 750 μL 1 mM dUTP (USB) .03 μL 300 μL dH₂O 0.5275 μL5.275 ml 0.9625 μL

0.0375 μL of φ29 was added to 1 well of 3× master mix prior to MDA (i.e.for a 384 well plate added

-   14.4 ul of φ29 to master mix). 0.03 μL per well of 1 mM random 9-mer    was added directly to DNA during the denaturation step.

1 μL of the MDA mix was added to each well and spun down briefly. Thealiquots were incubated at 26° C. for approximately 120 minutes toachieve about 10-30K amplification to 3-10 ng/w2ell.

φ29 was inactivated by incubating at 45-65° C. for five minutes.

Example 7 Complete Diploid Genome Sequence of Yoruban Female Using LFR

The LFR approach eliminates some of the problems associated with shortread sequencing because it is equivalent to single molecule sequencingof fragments >10 kb (up to 1 Mb is possible). This is achieved by therandom separation of corresponding parental DNA fragments intophysically distinct pools. As the fraction of the genome in each pooldecreases to less than a haploid genome, the statistical likelihood ofhaving a fragment from both parental chromosomes in the same pooldramatically diminishes (i.e., at 0.1 genome equivalents per well thereis a 10% chance that two fragments will overlap and a 50% chance thosefragments will be derived from separate parental chromosomes resultingin a 5% overall chance that a particular well will be uninformative fora given fragment). Likewise, the more individual pools interrogated thegreater number of times a fragment from the maternal and paternalcomplements will be analyzed (i.e., a 384 well plate with 0.1 genomeequivalents in each well results in a theoretical 19× coverage of boththe maternal and paternal alleles of each fragment). Ultimately, theentirety of all chromosomes from one parent is expected to be separatedfrom the corresponding chromosomes of the other parent in the majorityof the aliquots sequenced.

Several steps of preparation were used to generate these physicallyisolated fragments for analysis by any short read sequencing platform.First, a highly uniform amplification using a modified φ29-basedmultiple displacement amplification (MDA) was performed to increase thenumber of each fragment to >1000 copies per well. This step could beomitted for single molecule sequencing methods. Next, through a processof five enzymatic steps within each well, without any interveningpurification steps, DNA is fragmented and ligated with barcode adapters.Briefly, long DNA molecules were fragmented to blunt ended 300-1,300 bpsegments through the novel process of Controlled Random Enzymaticfragmenting (CoRE). CoRE fragments DNA through removal of uridine bases,incorporated at a predefined frequency during MDA, by uracil DNAglycosylase and endonuclease IV. Nick translation with E. colipolymerase 1 resolved the fragments and generated blunt ends. Uniquebarcode adapters designed to reduce any bias caused by differences insequence and concentration of each barcode were then ligated tofragmented DNA in each well using a high yield, low chimera formationprotocol. At this point all 384 wells were combined and an unsaturatedpolymerase chain reaction using primers common to the ligated adapterswere employed if necessary to generate sufficient template for shortread sequencing platforms.

To demonstrate the ability of LFR to determine a diploid genome sequencea library was generated starting from high molecular weight genomic DNAfrom an immortalized B-cell line of Yoruban female HapMap sampleNA19240. NA19240 was extensively interrogated as part of a trio (NA19240is the daughter of samples NA19238 and NA19239) in the HapMap and 1,000Genomes Projects. As a result, highly accurate haplotype information wasgenerated based upon the sequence data for parental samples NA19238 andNA19239. A total of ˜130 picograms of DNA (equivalent to ˜20 cells) werealiquoted into a 384-well plate. DNA in each well was tagged with adistinct 6-base sequence and sequenced using Complete Genomics' DNAnanoarray sequencing platform. 35 base mate-paired reads were mapped tothe reference genome using a custom alignment algorithm yielding 236 Gbof mapped data and an average genomic coverage of 86 fold.

Mapped reads from each well were then grouped based on unique 6 basebarcode identifiers and assembled into paternal and maternal chromosomalfragments. These fragment sizes were had a median of ˜90 kb and amaximum >180 kb. Using a two step custom haplotyping algorithm,overlapping heterozygous SNPs between fragments from the same parentalchromosome located in different wells were used to assemble largecontigs with an N50 of 373 Kb and an upper bound of 2.63 Mb. In totalalmost 2.7 million heterozygous SNPs were phased and approximately 86%of the genome of NA19240 was covered by LFR haplotypes.

To confirm the accuracy of LFR haplotype calls a low coverage BAClibrary was made and 10 clones that overlapped an average of 83 kb withLFR contigs were selected for further validation. Sequencing wasperformed at approximately 10 different heterozygous SNPs spread acrosseach BAC. 128 out of 130 informative SNPs were in perfect agreement withLFR calls resulting in a discrepancy rate of only 1.5%. To furthervalidate the LFR results, the SNP phasing data was compared to thosegenerated from parental sequencing. In general the two sets of data werehighly correlated.

To generate complete haplotypes of all NA19240 chromosomes (singlecontigs per parental chromosome comprising almost all heterozygous SNPs)we combined the LFR data with haplotypes derived from the sequences ofthe mother and of the father. To achieve this whole chromosome sparsehaplotypes were established using informative variants from one or bothparents and NA19240. This allowed phasing of about 1.8 million SNPs.Chromosome scaffolds were then used to phase haplotype contigs generatedby LFR resulting in high density whole chromosome haplotypesencompassing 2.6 million SNPs. It is estimated that ˜5% of heterozygousSNPs were detected but remained unphased and ˜5% were undetected.

Example 8 Ligation of Combinatorial Adaptors to DNA Fragments

In a first step, adaptor “A” was ligated to both sides of genomic DNAfragments in a reaction using T4 ligase. Ligation was conducted at 14°C. for two hours. The DNA:adaptor ratio was ˜30:1. The followingconcentrations of reactants were used for this first step of theprocess:

Adaptor A ligation 1 x DNA 15.60 ng/μl 40 μl HM Lig    3 x 28.4 μl Bfr.T4 Lig.   600 U/μl 2.1 μl Adaptor    5 uM 14.8 μl H2O μl Volume 85.3 μl

The partially-tagged DNA fragments were denatured and then annealed toprimers complementary to Adaptor A. The polymerase extends from theprimer to result in double stranded fragments, each tagged with anadaptor on one end. The following concentrations of reactants were usedfor this step of the process:

PfuCx 1 x Lig. DNA 12.0 ng/ul 40 μl PfuCx   2 x 40 μl mix3 ON904   20 uM 2 μl PfuCx  2.5 U/μl 1.6 μl  volume 83.6 μl  

The protocol used with the above reactants was incubation at 95° C. for3 minutes, 55° C. for 1 minute, and 72° C. for 10 minutes, then a rampdown to 4° C.

The next step of the process ligated adaptor B to the blunt end createdduring primer extension. Again, the mixture was incubated at 14° C. for2 hours. The DNA:adaptor B ratio was ˜15:1. The following concentrationsof reactants were used for this step of the process:

Adaptor B ligation 1 x PfuCx 19.00 ng/μl  40 μl DNA HM Lig    3 x 28.4μl  Bfr. T4 Lig.   600 U/μl 2.1 μl Ad119_3′    5 uM 7.4 μl H2O 2.1 μlVolume  80 μl

The present specification provides a complete description of themethodologies, systems and/or structures and uses thereof in exampleaspects of the presently-described technology. Although various aspectsof this technology have been described above with a certain degree ofparticularity, or with reference to one or more individual aspects,those skilled in the art could make numerous alterations to thedisclosed aspects without departing from the spirit or scope of thetechnology hereof. Since many aspects can be made without departing fromthe spirit and scope of the presently described technology, theappropriate scope resides in the claims hereinafter appended. Otheraspects are therefore contemplated. Furthermore, it should be understoodthat any operations may be performed in any order, unless explicitlyclaimed otherwise or a specific order is inherently necessitated by theclaim language. It is intended that all matter contained in the abovedescription and shown in the accompanying drawings shall be interpretedas illustrative only of particular aspects and are not limiting to theembodiments shown. Unless otherwise clear from the context or expresslystated, any concentration values provided herein are generally given interms of admixture values or percentages without regard to anyconversion that occurs upon or following addition of the particularcomponent of the mixture. To the extent not already expresslyincorporated herein, all published references and patent documentsreferred to in this disclosure are incorporated herein by reference intheir entirety for all purposes. Changes in detail or structure may bemade without departing from the basic elements of the present technologyas defined in the following claims.

1. A method of fragmenting genomic DNA in a sample, the methodcomprising: (a) dividing the sample into a plurality of separatealiquots; (b) amplifying genomic DNA in the separate aliquots to producea plurality of amplicons, wherein the amplifying is conducted with apopulation of dNTPs containing dNTP analogs, whereby a number ofnucleotides in the amplicons are dNTP analogs; (c) removing the dNTPanalogs from the amplicons to form gapped DNA; and (d) treating thegapped DNA such that gaps on opposite strands converge, thereby creatingblunt-ended DNA fragments.
 2. The method of claim 1, wherein thepopulation comprises at least two different dNTP analogs.
 3. The methodof claim 1, wherein the population comprises dUTP and 5-methyl dCTP. 4.The method of claim 1, wherein the separate aliquots are droplets.
 5. Amethod of fragmenting a sample of DNA, comprising: (a) dividing thesample into a plurality of separate aliquots; (b) amplifying DNA in theseparate aliquots to form a plurality of amplicons, wherein theamplifying is conducted with a population of dNTPs, wherein thepopulation of dNTPs comprises: (i) a predetermined ratio of dUTP todTTP, such that a number of thymines in the DNA are replaced by uracils,and (ii) a predetermined ratio of 5-methyl dCTP to dCTP, such that anumber of cytosines are replaced by 5-methyl cytosines, (c) removing theuracils and the 5-methyl cytosines from the amplicons to form gappedDNA, (d) treating the gapped DNA such that gaps on opposite strandsconverge, thereby creating blunt-ended DNA fragments.
 6. The method ofclaim 5, wherein the method further comprises obtaining a number ofsequence reads from DNA fragments of each separate aliquot.
 7. Themethod of claim 5, the method further comprising dividing the DNAamplified in step (b) into a second tier of separate aliquots.
 8. Themethod of claim 7, the method further comprising obtaining a number ofsequence reads from fragments of each separate aliquot in the secondtier.
 9. The method of claim 5, wherein the separate aliquots have avolume of less than 100 nL.
 10. The method of claim 5, wherein step (b)is conducted in the presence of a member selected from glycogen-dimethylsulfoxide (DMSO), Extreme Thermostable Single-Stranded DNA BindingProtein (ET SSB), trimethylglycine (TMG) (betaine), and any combinationthereof.
 11. A method of fragmenting a sample of double-stranded targetDNA, the method comprising: (a) dividing the sample into separatealiquots, (b) amplifying DNA in the separate aliquots to form aplurality of amplicons, wherein (i) the amplifying is conducted with apopulation of dNTPs that comprises dNTP analogs, such that a number ofnucleotides in the DNA are dNTP analogs, and (ii) the amplifying isconducted in the presence of an additive selected from glycogen,dimethyl sulfoxide (DMSO), Extreme Thermostable Single-Stranded DNABinding Protein (ET SSB), trimethylglycine (TMG) (betaine), and anycombination thereof, (c) removing the dNTP analogs from the amplicons toform gapped DNA, (d) treating the gapped DNA acid to translate the gapsuntil gaps on opposite strands converge, thereby creating blunt-endedDNA fragments.
 12. The method of claim 11, wherein the method furthercomprises (e) obtaining a number of sequence reads from fragments ofeach separate aliquot.
 13. The method of claim 12, wherein prior to step(e), the fragments of each separate aliquot are amplified a second time.14. The method of claim 11, wherein the population comprises a pluralityof different dNTP analogs.
 15. The method of claim 11, wherein thepopulation comprises dUTP and 5-methyl dCTP.
 16. The method of claim 11,wherein the separate aliquots are droplets.
 17. A method for reducing GCbias when sequencing a sample of genomic DNA, wherein the sequencingcomprises: (i) dividing the sample into a plurality of separatealiquots; (ii) amplifying genomic DNA in the separate aliquots toproduce a plurality of amplicons, (iii) combining the amplicons from aplurality of the aliquots into a mixture; (iv) obtaining sequence readsfrom amplicons in the mixture; and (v) assembling the sequence readsinto assembled sequence information by a process that comprisesdetermining the mixtures of origin from which the sequence reads wereobtained; wherein the method of reducing GC bias comprises: (a)conducting the amplifying in step (ii) in the presence of a combinationof nucleotides containing dNTP analogs, such that some of thenucleotides incorporated into the amplicons are dNTP analogs; and then(b) removing the dNTP analogs from the amplicons to form gapped DNA. 18.The method of claim 17, further comprising treating the gapped DNA aciduntil gaps on opposite strands converge, thereby creating blunt-endedDNA fragments.
 19. The method of claim 17, wherein the combinationcomprises at least two different dNTP analogs.
 20. The method of claim17, wherein the combination comprises dUTP and 5-methyl dCTP.